Single-cell genomic methods to generate ex vivo cell systems that recapitulate in vivo biology with improved fidelity

ABSTRACT

Disclosed here is a generally applicable framework that utilizes massively-parallel single-cell RNA-seq to compare cell types/states found in vivo to those of in vitro models. Furthermore, Applicants leverage identified discrepancies to improve model fidelity. Applicants uncover fundamental gene expression differences in lineage-defining genes between in vivo systems and in vitro systems. Using this information, molecular interventions are identified for rationally improving the physiological fidelity of the in vitro system. Applicants demonstrated functional (antimicrobial activity, niche support) improvements in Paneth cell physiology using the methods.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims the benefit of U.S. Provisional Application Nos. 62/613,710, filed Jan. 4, 2018, and 62/702,168, filed Jul. 23, 2018. The entire contents of the above-identified applications are hereby fully incorporated herein by reference.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH

This invention was made with government support under Grant Nos. DE013023, HL095722, OD020839, AI089992, CA217377, AI039671, AI118672, HG006193 and CA202820 awarded by the National Institutes of Health. The government has certain rights in the invention.

REFERENCE TO AN ELECTRONIC SEQUENCE LISTING

The contents of the electronic sequence listing (BROD-2417.ST25.txt”; Size is 8 Kilobytes and it was created on Jan. 2, 2019) is herein incorporated by reference in its entirety.

TECHNICAL FIELD

The subject matter disclosed herein is generally directed to ex vivo cell-based systems that faithfully recapitulate an in vivo phenotype of interest and methods of generating and using the cell-based systems.

BACKGROUND

Intestinal organoids, derived from intestinal stem cells (ISCs) and composed of ISCs, Paneth cells (PCs), enteroendocrine cells (EECs), goblet cells and absorptive enterocytes, have been invaluable to the study of intestinal biology [1]. Recent advances in massively-parallel single-cell RNA-sequencing (scRNA-seq) have enabled [2] the cataloging of cell types and states of the murine small intestinal epithelium [3] and intestinal organoids [4], offering extensive insight into tissue heterogeneity; specifically within subsets of rare secretory cell populations. Indeed, the generation of comprehensive cellular atlases has become a major focus of a global effort seeking to map tissues in humans, model organisms, and derived organoids at single-cell resolution [5]. The ability to reconstruct tissues with a “bottom-up” unbiased approach will undoubtedly yield key insights into their cellular constituents [6,7].

To improve the representation of specific cell types in organoids, investigators have utilized cellular engineering approaches starting with ISCs to derive multiple enriched or specialized models. These include enterocytes with improved intestinal ion transport [8], epithelial monolayers capable of secretion and IgA transcytosis [9], and organoids enriched for the rare secretory EEC population [10]. However, there has been no formal comparison of the extent to which conventional intestinal organoids, or further specialized models, recapitulate defined in vivo cell types and states. Moving beyond the generation of in vivo tissue maps towards mechanistic insights, particularly in disease settings, will require an understanding of how the in vitro organoid models utilized for such studies represent the cell types and states identified.

Recent work has demonstrated the utility of organoids in assessing how genetic mutations impact the overall regenerative and/or tumorigenic capacity of ISCs [11,12]. However, their application to the study of polygenic inflammatory disease has been more complex. While cancer-causing mutations appear as a readily visible phenotype in organoids derived from stem cells which uniformly harbor these mutations [12], subtler phenotypes, such as those present in inflammatory bowel disease (IBD), may not manifest if the correct cell state present in vivo is not accurately represented within an organoid. This challenge is particularly clear in IBD [13], where loci identified through genome wide association study (GWAS) have proven difficult to efficiently examine through the use of in vivo animal models.

PC dysfunction is implicated in Crohn's disease, a subset of IBD typically afflicting the small bowel [14]. Co-localized with, LGR⁵ ISCs of the small intestinal crypts, long-lived PCs [15] support maintenance of the ISC niche, producing the Wnt and Notch signaling ligands WNT3, WNT3A, and DLL4 [16] and are potent modulators of the gut microflora through secretion of multiple antimicrobials including lysozyme (LYZ), phospholipase A2 group 1B (PLA2G1B), angiogenin ribonuclease A family member 5 (ANG5), and alpha-defensins (DEFAs), amongst others [17]. Allelic variants of NOD2, ATG16L1, and XBP1, are associated with inflammation, barrier dysfunction, and microbial dysbiosis in IBD through altered function in PCs [18-21]. Risk variants of NOD2 result in lower DEFA expression [22], murine knockout (KO) or alteration of autophagy gene ATG16L1 leads to defects in autophagy, granule formation, and secretion [21,23], and KO of the ER stress response gene XBP1 results in a total absence of PCs due to uncompensated ER stress [24]. While in vivo models currently provide the most physiologically-representative system to probe PC biology, they are inherently complex and poorly scaled, hindering basic research and therapeutic lead identification.

Existing in vitro models have also proven inherently limited. Ex vivo fresh crypt isolates, which were used to identify the secretion of antimicrobials in response to host stimuli [25,26], are unstable and as such restricted to brief experimental windows. A more sustainable and scalable approach using Caco2 cells differentiated to a PC proxy, has elucidated the role of NOD2 in antimicrobial production [27]. However, the phenotype of these induced PCs is not established. Recently, conventional intestinal organoids were used to describe the dynamics of PC degranulation in response to multiple agonists [28] and to assess PC suppression of enteric pathogens [29]. While these organoid studies are arguably more representative than other in vitro systems, the question of physiological fidelity of this heterogeneous system remains unanswered.

Thus, in vitro systems that faithfully recapitulate an in vivo phenotype and methods of obtaining such systems are needed.

SUMMARY

Single-cell genomic methods provide unprecedented resolution for characterizing the component cell types/states of tissues, such as the epithelial subsets of the gastrointestinal tract. Nevertheless, functional studies of these subsets at scale require faithful ex vivo and in vitro models of identified in vivo biology. While organoids have been invaluable in providing mechanistic insights in vitro, the extent to which organoid-derived cell types, and other ex vivo models, recapitulate their in vivo counterparts remains untested, with no systematic approach for improving model fidelity.

Here, Applicants present a generally applicable framework that utilizes massively-parallel single-cell RNA-seq to identify discrepancies in cell types/states of ex vivo cell-based systems, such as organoids, to those found in vivo models that the ex vivo cell-based systems are intended to emulate. Furthermore, Applicants leverage those identified discrepancies to improve model fidelity. Using the Paneth cell (PC), which supports the stem cell niche and produces the largest diversity of antimicrobials in the small intestine, as an exemplar, Applicants uncover fundamental gene expression differences in lineage-defining genes between in vivo PCs and those of the current in vitro organoid model. Using this information, Applicants nominated molecular interventions for rationally improving the biological fidelity of the in vitro PCs. Applicants then performed transcriptomic, cytometric, morphologic, and proteomic characterization, and demonstrated functional (antimicrobial activity, niche support) improvements in Paneth cell physiology.

This systematic approach provides a workflow for identifying the limitations of ex vivo models and enhancing their biological fidelity. Using adult stem cell-derived organoids as a model system, Applicants successfully generated a structurally and physiologically representative in vitro PC population, enabling studies of host-microbe interactions, cellular development, and disease. The generation of rationally-improved cellular models will facilitate mechanistic exploration of specific disease-associated genes in their respective cell types.

In one aspect, the present invention provides for a method of generating an ex vivo cell-based system that faithfully recapitulates an in vivo phenotype of interest comprising: determining, using single cell RNA sequencing, one or more cell types or one or more cell states in an initial cell-based system; identifying differences in one or more cell types and/or cell states between the initial cell-based system and a target in vivo system having the phenotype of interest; and modulating the initial cell-based system to induce a shift in cell type and/or cell states that reduces the distance in gene expression space between the initial cell-based system and the in vivo system.

In certain embodiments, the gene expression space comprises 10 or more genes, 20 or more genes, 30 or more genes, 40 or more genes, 50 or more genes, 100 or more genes, 500 or more genes, or 1000 or more genes. In certain embodiments, the expression space defines one or more cell pathways. In certain embodiments, the expression space is a transcriptome of the target in vivo system.

In certain embodiments, identifying differences in cell type and/or cell states between the initial cell-based system and the target in vivo system comprises comparing a gene expression distribution as determined by single cell RNA sequencing of the initial cell-based system and a gene expression distribution as determined by single cell RNA sequencing of the ex vivo system.

In certain embodiments, the distance is measured by a Euclidean distance, Pearson coefficient, Spearman coefficient, or combination thereof.

In certain embodiments, the shift in cell type and/or cell states that reduces the distance in gene expression space in the initial cell-based system is a statistically significant shift in the gene expression distribution of the initial cell-based system toward that of the in vivo system. The statistically significant shift may be at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%. The statistical shift may include the overall transcriptional identity or the transcriptional identity of one or more genes, gene expression cassettes, or gene expression signatures of the ex vivo system compared to the in vivo system (i.e., at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% of the genes, gene expression cassettes, or gene expression signatures are statistically shifted in a gene expression distribution). A shift of 0% means that there is no difference to the in vivo system. A gene distribution may be the average or range of expression of particular genes, gene expression cassettes, or gene expression signatures in the ex vivo or in vivo system (e.g., a plurality of a cell of interest from an in vivo subject may be sequenced and a distribution is determined for the expression of genes, gene expression cassettes, or gene expression signatures). In certain embodiments, the distribution is a count-based metric for the number of transcripts of each gene present in a cell. A statistical difference between the distributions indicates a shift. The one or more genes, gene expression cassettes, or gene expression signatures may be selected to compare transcriptional identity based on the one or more genes, gene expression cassettes, or gene expression signatures having the most variance as determined by methods of dimension reduction (e.g., tSNE analysis). In certain embodiments, comparing a gene expression distribution comprises comparing the initial cells with the lowest statistically significant shift as compared to the in vivo system (e.g., determining shifts when comparing only the ex vivo cells with a shift of less than 95%, less than 90%, less than 85%, less than 80%, less than 75%, less than 70%, less than 65%, less than 60%, less than 55%, less than 50%, less than 45%, less than 40%, less than 35%, less than 30%, less than 25%, less than 20%, less than 15%, less than 10% to the in vivo system).

In certain embodiments, the method may further comprise modulating the initial cell-based system to induce a gain of function in addition to the in vivo phenotype of interest comprising modulating expression of one or more genes, gene expression cassettes, or gene expression signatures associated with the gain of function. In certain embodiments, the method may further comprise modulating the initial cell-based system to induce a loss of function in addition to the in vivo phenotype of interest comprising modulating expression of one or more genes, gene expression cassettes, or gene expression signatures associated with the loss of function.

In certain embodiments, modulating comprises increasing or decreasing expression of one or more genes, gene expression cassettes, or gene expression signatures. In certain embodiments, modulating comprises activating or inhibiting one or more genes, gene expression cassettes, or gene expression signatures (e.g., with an agonist or antagonist).

In certain embodiments, the initial cell-based system comprises a single cell type or sub-type, a combination of cell types and/or subtypes, cell-based therapeutic, an explant, or an organoid.

In certain embodiments, the single cell type or subtype or combination of cell types and/or subtypes comprises an immune cell, intestinal cell, liver cell, kidney cell, lung cell, brain cell, epithelial cell, endoderm cell, neuron, ectoderm cell, islet cell, acinar cell, oocyte, sperm, hematopoietic cell, hepatocyte, skin/keratinocyte, melanocyte, bone/osteocyte, hair/dermal papilla cell, cartilage/chondrocyte, fat celliadipocyte, skeletal muscular cell, endotheliumn cell, cardiac muscle/cardiomvocyte, trophoblast, tumor cell, or tumor microenvironment (TME) cell.

In certain embodiments, the single cell type or sub-type is pluripotent, or the combination of cell types and/or subtypes comprises one or more stem cells. The one or more stem cells may be selected from the group consisting of lymphoid stem cells, myeloid stem cells, neural stem cells, skeletal muscle satellite cells, epithelial stem cells, endodermal and neuroectodermal stem cells, germ cells, extraembryonic and embryonic stem cells, mesenchymal stem cells, intestinal stem cells, embryonic stem cells, and induced pluripotent stem cells (iPSCs).

In certain embodiments, the cell-base therapy comprises iPSCs, autologous T cells, CAR T cells, suppressive T cells or tissue transplants. The cell based therapy may comprise adoptive cell transfer (ACT) of T cells. The T cells may be activated or effector T cells specific for a tumor antigen. The cell based therapy may provide cells for regeneration of tissue types or replacement or supplementation of diseased cell types. The cells may be ex vivo cells of the tissue type or stem cell types capable of differentiation into the target tissue.

In certain embodiments, the initial cell-based system is derived from a subject with a disease (e.g., to study the disease ex vivo). The disease may be selected from the group consisting of cancer, autoimmune disease, bone marrow failure, hematological conditions, aplastic anemia, beta-thalassemia, diabetes, motor neuron disease, Parkinson's disease, spinal cord injury, muscular dystrophy, kidney disease, liver disease, multiple sclerosis, congestive heart failure, head trauma, lung disease, psoriasis, liver cirrhosis, vision loss, cystic fibrosis, hepatitis C virus, human immunodeficiency virus, inflammatory bowel disease (IBD), and any disorder associated with tissue degeneration.

In certain embodiments, modulating the initial cell-based system comprises delivering one or more modulating agents that modify expression of one or more cell types or states in the initial cell-based system, delivering an additional cell type or sub-type to the initial cell-based system, or depleting an existing cell type or sub-type from the initial cell-based system. The one or more modulating agents may comprise one or more cytokines, growth factors, hormones, transcription factors, metabolites or small molecules. The one or more modulating agents may be a genetic modifying agent or an epigenetic modifying agent. The genetic modifying agent may comprise a CRISPR system, a zinc finger nuclease system, a TALEN, or a meganuclease. The epigenetic modifying agent may comprise a DNA methylation inhibitor, HDAC inhibitor, histone acetylation inhibitor, histone methylation inhibitor or histone demethylase inhibitor.

In certain embodiments, the one or more modulating agents modulate one or more cell-signaling pathways. The one or more pathways may comprise Notch signaling. The one or pathways may comprise Wnt signaling.

In certain embodiments, the ex vivo cell-based system comprises Paneth cells and the one or more agents comprise a Wnt signaling activator and Notch signaling inhibitor. The Wnt signaling activator may comprise CHIR99021. The Notch signaling inhibitor may comprise DAPT.

In certain embodiments, the method may further comprise: transplanting the initial cell-based system into an animal model; recovering cells from the transplanted cell-based system; performing single cell RNA sequencing on the recovered cells; and measuring statistically significant shifts in gene expression distribution compared to the in vivo system. Thus, the transplanted cells can be revaluated for fidelity compared to an in vivo system.

In another aspect, the present invention provides for an ex vivo cell-based system derived from the method according to any embodiment herein.

In another aspect, the present invention provides for use of the cell based system of any embodiment herein to identify a therapeutic agent or determine the efficacy of a therapeutic agent.

In another aspect, the present invention provides for use of the cell based system of any embodiment herein to select one or more therapeutic agents for treatment of a subject in need thereof.

In another aspect, the present invention provides for use of the cell based system of any embodiment herein to screen for one or more on-target or off-target genetic modifications.

In another aspect, the present invention provides for an ex vivo cell-based system derived from any embodiment herein, wherein the single cell type or subtype or combination of cell types and/or subtypes comprises a tumor cell. In another aspect, the present invention provides for an ex vivo cell-based system derived from any embodiment herein, wherein the single cell type or subtype or combination of cell types and/or subtypes comprises a tumor microenvironment cell. The tumor microenvironment cell may be a tumor infiltrating lymphocyte (TIL). The single cell type or subtype or combination of cell types and/or subtypes may faithfully recapitulate a phenotype from a subject responsive to cancer treatment. The single cell type or subtype or combination of cell types and/or subtypes may faithfully recapitulate a phenotype from a subject non-responsive to cancer treatment. The treatment may be an immunotherapy. The immunotherapy may be checkpoint blockade therapy (CBT). The single cell type or subtype or combination of cell types and/or subtypes may faithfully recapitulate a phenotype from a subject with a cancer recurrence.

In another aspect, the present invention provides for an ex vivo cell-based system derived from any embodiment herein, wherein the single cell type or subtype or combination of cell types and/or subtypes comprises an in vitro fertilized egg that faithfully recapitulates the phenotype of an in vivo fertilized egg. Not being bound by a theory, prior to the present invention it was unknown whether an in vitro fertilized egg faithfully recapitulates the phenotype of an in vivo fertilized egg.

In another aspect, the present invention provides for an ex vivo cell-based system derived from any embodiment herein, wherein the system is an organoid model selected from the group consisting of an intestinal, liver, kidney, lung, or brain organoid model.

In another aspect, the present invention provides for use of the system of any embodiment herein in a method for adoptive cell transfer (ACT), wherein a single cell type or subtype or combination of cell types and/or subtypes from the ex vivo cell-based system are transferred to a subject in need thereof. The subject may have a disease selected from the group consisting of cancer, autoirmnnune disease, bone marrow failure, hemrnatological conditions, aplastic anemia, beta-thalassemia, diabetes, motor neuron disease, Parkinson's disease, spinal cord injury, muscular dystrophy, kidney disease, liver disease, multiple sclerosis, congestive heart failure, head trauma, lung disease, psoriasis, liver cirrhosis, vision loss, cystic fibrosis, hepatitis C virus, human immunodeficiency virus, inflammatory bowel disease (IBD), and any disorder associated with tissue degeneration.

In certain embodiments, T cells that faithfully recapitulate an in vivo phenotype of interest are transferred to a subject suffering from cancer or an autoimmune disease (e.g., activated, effector, or suppressive T cells). In certain embodiments, cells for regenerating a tissue are transferred (e.g., tissue cells or stem cells).

In another aspect, the present invention provides for use of the system of any cancer ex vivo system herein in a method for screening modulating agents. In another aspect, the present invention provides for use of the system of any cancer ex vivo system herein in a method for screening agents having antitumor activity. The cancer cells may be screened for agents capable of modulating an immune evasion phenotype (e.g., the tumor cells can evade the immune system). In certain embodiments, immune cells may be screened for antitumor cell activity. The immune cells may be screened for antitumor activity against an ex vivo tumor cell system.

In another aspect, the present invention provides for a method of screening for agents capable of modulating Paneth cell activity comprising: treating EGF, Noggin, R-spondin 1, CHIR99021 and DAPT (ENR+CD) cells with a stimulant capable of inducing Paneth cell secretion and an agent; and measuring Paneth cell antimicrobial secretion.

In another aspect, the present invention provides for a method of screening for agents capable of modulating Paneth cell antibacterial activity comprising: suspending EGF, Noggin, R-spondin 1, CHIR99021 and DAPT (ENR+CD) cells with bacteria and an agent; and measuring bacterial growth.

In another aspect, the present invention provides for a method of producing an in vitro Paneth cell enriched gut organoid system comprising: culturing an LGR5+ ISC-enriched population of cells in a hydrogel matrix in the presence of EGF, Noggin, R-spondin 1, CHIR99021 and valproic acid (ENR+CV); culturing the ENR+CV cells in the presence of EGF, Noggin, R-spondin 1, CHIR99021 and DAPT (ENR+CD); and modulating the activity of one or more nuclear receptors selected from the group consisting of progesterone receptor (PR), aldosterone receptor (AR) and glucocorticoid receptor (GR). In another aspect, the present invention provides for a cell obtained from by the method of above.

These and other aspects, objects, features, and advantages of the example embodiments will become apparent to those having ordinary skill in the art upon consideration of the following detailed description of illustrated example embodiments.

BRIEF DESCRIPTION OF THE DRAWINGS

An understanding of the features and advantages of the present invention will be obtained by reference to the following detailed description that sets forth illustrative embodiments, in which the principles of the invention may be utilized, and the accompanying drawings of which:

FIGS. 1A-1I—Transcriptional benchmarking of in vitro Paneth cells to in vivo FIG. 1A) Schematic of intestinal epithelial cell isolation from terminal ileum for unbiased identification of in vivo Paneth cell (PC) signature genes, and system for intestinal stem cell (ISC) enrichment to characterize in vitro PCs, via high-throughput scRNA-seq. FIG. 1B) Marker gene overlay for binned count-based expression level (log(scaled UMI+1)) of Lyz1, a canonical PC marker gene, on a tSNE (t-stochastic neighbor embeddin FIG. 1G) plot of 7,667 small intestinal epithelial cells isolated from the terminal ileum; receiver operating characteristic (ROC)-test area under the curve (AUC)=0.995, n=2 mice, independent experiments (Table S1). FIG. 1C) Violin plot for the count-based expression level (log(scaled UMI+1)) of Lyz1 across clusters identified through shared nearest neighbor (SNN) analysis (see Methods) over small intestinal epithelial cells; n=196 cells in cluster 11, 7,667 cells total. FIG. 1D) A tSNE plot of 2,513 cells, with clusters identified through SNN (Table S1 for full gene lists with ROC>0.60) from conventional ENR organoids; n=6 wells of ENR organoids. FIG. 1E) Marker gene overlay for binned count-based expression level (log(scaled UMI+1)) of Lyz1 on a tSNE plot from (FIG. 1D); ROC-test AUC=0.856. FIG. 1F) Violin plot of expression contribution to a cell's transcriptome of PC genes across ENR organoid clusters from (FIG. 1D) (In vivo PC gene list AUC>0.65, Table Si); effect size 0.721, ENR-4 vs all ENR, *t-test p<2.2×10⁻¹⁶ FIG. 1G) Row-normalized heatmap of top differentially expressed genes using bimodal test over single-cells from the top 200 PC-like cells from ENR-4 and the 196 in vivo PCs (cluster 11, from (FIG. 1C)); *bimodal test, all displayed genes p<1.89×10⁻¹⁶ or less with Bonferroni correction. FIG. 1H) Violin plots for the count-based expression level (log(scaled UMI+1)) of Lyz1, Ang4, and Defa3 in ENR and in vivo PCs; *bimodal test, all p<2.92×10⁻³⁷ or less with Bonferroni correction FIG. 1I) Violin plot of expression contribution to a cell's transcriptome of PC genes (effect size 1.25, InVivo vs. ENR, *t-test p<2.2×10⁻¹⁶), Wnt pathway (effect size 0.559, InVivo vs. ENR, *t-test p<2.035×10⁻⁸) and Notch pathway (effect size −0.500, InVivo vs. ENR, *t-test p<5.25×10⁻⁷) genes (see Table S2 for gene lists).

FIGS. 2A-2E—Establishing chemically-induced PC-enriched cultures FIG. 2A) Schematic of small molecule-driven differentiation of LGR5+ ISCs (C—CHIR99021, D—DAPT) and non-specific differentiation. FIG. 2B) mRNA expression of PC (Lyz1, Defal, Mmp7) and ISC (Lgr5) markers relative to ENR, for ENR+CV and ENR+CD at two (D2), four (D4), and six days (D6) (n=3 biological replicates; 2-way ANOVA with multiple comparison test versus ENR; ** adj. p<0.01, *** adj. p<0.001). FIG. 2C) Representative confocal imaging of whole cell clusters for PC antimicrobials following six days in ENR+CD versus ENR and ENR+CV: stained for anti-DEFA, anti-LYZ and counterstained with DAPI and for actin (phalloidin). FIG. 2D) High-resolution fluorescent imaging of in vivo and in vitro single cells from six-day culture in ENR+CD shows similar morphology and antimicrobial expression: stained for DEFA, LYZ and counterstained with DAPI and for actin (phalloidin). FIG. 2E) Viable cell populations from ENR, ENR+CD, and ENR+CV precursor culture have distinct populations based on CD24 and LYZ content, indicative of PC maturity (n=3 biological replicates).

FIGS. 3A-3F—Characterizing the in vitro PC proteome FIG. 3A) Samples used to interrogate the PC-enriched proteomes of ENR+CD- and ENR-treated cells by high resolution, accurate mass LC-MS/MS-based proteomics, including sample nomenclature. FIG. 3B) Volcano plot of differentially regulated proteins between six day (6D) ENR+CD and ENR cells shows clear enrichment in secreted and PC-associated proteins (labeled). Cut-offs are 2 standard deviations outside the mean expression level of the set and FDR<0.05. FIG. 3C) Rank-order log fold change of detected PC antimicrobial proteins (AMPs) and secretory proteins associated with enteroendocrine and goblet lineages demonstrates differential regulation of AMP classes between ENR+CD and ENR cultures, as well as enrichment in PC and enteroendocrine proteins. FIG. 3D) Protein variation by sample for ENR+CD- and ENR-enriched proteins demonstrated by coefficient of variation (CoV) vs. fold change relative to the median expression of the enriched proteins in ENR+CD and ENR samples for each replicate. FIG. 3E) PC normalized enrichment score (NES) for the full rank-ordered ENR+CD/ENR proteome by GSEA using the top 500 genes from de facto in vivo PC gene set (Sato et al. 2011). FIG. 3F) GSEA enrichment map of transcription factors linked to ENR+CD- and ENR-enriched proteins following a moderately conservative cutoff of p-value <0.005, FDR<0.075, and overlap coefficient of 0.2.

FIGS. 4A-4E—Single-cell RNA-sequencing reveals cellular composition across treatments and origins of proteomic data FIG. 4A) A tSNE plot of single cells derived from ENR+CV (n=985 cells), ENR (n=2544 cells), and ENR+CD (n=2382 cells) harvested at day 6 of differentiation, colored by treatment; n=6 wells for each condition. FIG. 4B) Marker gene overlays (on plot from (FIG. 4A)) for binned count-based expression level (log(scaled UMI+1)) of individual genes of interest. FIG. 4C) A tSNE plot, with clusters identified through SNN graph-based clustering (see Table S1 for marker gene lists), highlighting distinct cell states within each organoid; opacity of density clouds correspond to the Paneth cell score of ENR-4, ENR+CD-3, and ENR+CD-4 clusters (see FIG. 5B). FIG. 4D) Violin plot of expression contribution to a cell's transcriptome of ENR+CD proteome-enriched genes across organoid clusters from (FIG. 4C) (Table S1 for full gene list); effect size 2.40 ENR+CD-4 vs all cells, p<2.2×10⁻¹⁶ FIG. 4E) Frequency of each cluster observed within each organoid condition as a fraction of the total cells in each condition.

FIGS. 5A-5C—Transcriptional identity of Paneth cells within conditions and related to in vivo FIG. 5A) Violin plots for the count-based expression level (log(scaled UMI+1)) of selected genes across called clusters, colors correspond to clusters in FIG. 4C; *t-test, p<6.80×10⁻⁷⁴ or less with Bonferroni correction, for Lyz1, Defa24, Defa3, Mmp7 ENR+CD-4 relative to ENR-4 FIG. 5B) Violin plot of expression contribution to a cell's transcriptome of in vivo Paneth cell and enteroendocrine marker-cell genes (see Table S1 for full gene list, AUC>0.65); effect size 2.52 ENR+CD-4 vs. ENR-4, p<2.2×10⁻¹⁶ for Paneth cell score; effect size 0.0465, p=0.2339 ENR+CD-4 vs. ENR-4 for enteroendocrine cell score. FIG. 5C) Row-clustered heatmap of z-scores (−2.5 to 2.5; purple to yellow) for defining genes (n=69 with AUC>0.65 of in vivo Paneth cells, see Table S1 for full gene list) across top 200 cells for Paneth score (FIG. 5B) from ENR-4 and ENR+CD-4 conditions compared to two biological replicates of in vivo PCs from the terminal ileum (n=196 cells).

FIGS. 6A-6E—CI-PCs are functional in response to host and microbial stimuli FIG. 6A) Supernatant LYZ from 24-hr basal and 10 μm CCh-stimulated LYZ cells at varying number of days in ENR+CD culture (top). DNA content from matched samples (bottom) (n=8 well replicates; error bars too small to visualize). FIG. 6B) Supernatant LYZ from six day ENR+CD collected basally and following 10 μm CCh stimulation for 0.5, 2, 4, 6, and 24 hours (top). DNA content from matched samples basally and following 10 μm CCh stimulation (bottom) (n=8 well replicates). FIG. 6C) 24-hour basal (non-stimulated) and 10 μm CCh-stimulated LYZ secretion in six-day ENR+CD versus ENR and ENR+CV (n=8 well replicates; 2-way ANOVA with multiple comparison test; ns non-significant, * adj. p<0.05, **** adj. p<0.0001). FIG. 6D) 4-hour co-culture of freshly passaged six-day ENR and ENR+CD cells and select gram-negative and gram-positive aerobic bacteria (n=13 well replicates; 2-way ANOVA with multiple comparison test, * adj. p<0.05, *** adj. p<0.001, **** adj. p<0.0001). FIG. 6E) Normalized cellular viability, caspase activity per viable cell, and cytotoxicity per viable cell from 24-hour and 48-hour ENR & ENR+CD co-cultures at specified mixing ratios (n=3 biological replicates; one sample t-test,* p<0.05, ** p<0.01, *** p<0.001, **** p<0.0001).

FIGS. 71-7D—CI-PCs reveal putative function of Nupr1 transcription factor in PC survival FIG. 7A) ENR+CD is enriched for in vivo PC and EEC transcription factors, including Nupr1. FIG. 7B) Violin plots for the count-based expression level (log(scaled UMI+1)) of Nupr1 across in vivo and in vitro called clusters. FIG. 7C) Trifluorperazine (TFP) treatment concurrent with 6-day ENR+CD differentiation reveals dose-dependent toxicity, with preference to PCs (CD24+& LYZ+) and PC-like (CD24+, LYZ+) populations as assessed by flow cytometry.

FIG. 7D) Two-day trifluorperazine (TFP) treatment following 6-day ENR+CD differentiation reveals dose-dependent toxicity, with preference to PCs (CD24+& LYZ+) and PC-like (CD24+, LYZ+) populations as assessed by flow cytometry.

FIGS. 8A-8F—Image analysis of cell clusters and flow cytometry FIG. 8A) Bright-field microscopy after six days of ENR+CD culture shows annular morphology and darkened lumen of cell culusters consistent with presence of granule-rich cells. FIG. 8B) Percentage of total cells that are LYZ+ and DEFA+ following six days of ENR, ENR+CV, and ENR+CD culture (from cell counting of whole clusters) (n=3 minimum biological replicates, 1-way ANOVA with multiple comparison test versus ENR, **** adj. p<0.0001). FIG. 8C) Collapsed z-stack of whole cluster with individual cells highlighted (1-3) following six days of ENR+CD, stained for LYZ and DEFA and counterstained with DAPI and for actin (phalloidin). 1-3) Normalized mean-area intensity versus z-axis depth profiles of representative individual LYZ+/DEFA+co-staining cells.

FIG. 8D) Representative flow cytometry of ENR and ENR+CD at six days with distinct populations of CD24+ and LYZ+ cells indicative of phenotypic PCs. FIG. 8E) Representative gating for flow cytometry, including removal of doublets and non-viable cells in final gating. FIG. 8F) Percentage of viable cells (membrane impermeable) over time of ENR versus ENR+CD culture.

FIGS. 9A-9E—Proteomic pipeline and sample-to-sample comparison FIG. 9A) Schematic of proteomic analysis for samples: culture, collection, lysis, reduction and alkylation, proteolytic digestion, labeling of peptides with isobaric mass tag reagents (Tandem Mass Tags, TMT10-plex; Thermo), off-line fractionation by basic reverse phase chromatography, analysis of fractions by LC-MS/MS, identification of peptides and proteins using Spectrum Mill software (Agilent), and statistical analysis of the resulting data (moderated T-test) to identify confidently differential proteins. FIG. 9B) Gross distribution of fold change for individual protein replicate pairs (ENR+CD/ENR). Dashed lines identify two standard deviations (±2σ). FIG. 9C) Proteome sample correlation between all biological (n=2) and technical (n=2/biological) replicates. FIG. 9D) Sample overlap comparison of ENR+CD-enriched (+2σ) proteins. FIG. 9E) Sample overlap comparison of ENR-enriched (−2σ) proteins.

FIGS. 10A-10B—Structural and functional insights from the in vitro PC proteome FIG. 10A) ENR+CD-enriched proteins are well-annotated in the gene ontology (GO) database and show robust enrichment for functions and compartments of secretory cells determined by fold enrichment vs. FDR using DAVID. FIG. 10B) ENR-enriched proteins are well annotated in the gene ontology database (GO) and show enrichment for functions and compartments of transcriptionally and translationally active cells determined by fold enrichment vs. FDR using DAVID.

FIGS. 11A-11B—Quality metrics for single-cell RNA sequencing FIG. 11A) Total gene number of cells maintained in analyses with a lower cutoff of n=400 unique genes per cell. Total unique molecular identifiers (UMIs) used as the basis for cell-by-gene tables collapsed to UMI as input into Seurat with lower bound representing n=400 unique genes and upper bound 8000 UMIs. Note: Clusters ENR+CV-3, ENR+CV-4, and ENR-1 had significantly higher levels of genes and UMIs and, intriguingly, were also the three clusters with highest levels of Lgr5 (see FIG. 5A), indicating that stem cells may contain larger contents of RNA, as they are in a biosynthetic state before differentiation and maturation. FIG. 11B) Violin plot of expression contribution to a cell's transcriptome of mitochondrial and ribosomal genes across identified sub sets.

FIGS. 12A-12C—Signaling pathways and processes associated with in vitro PC enrichment FIG. 12A) Violin plot of expression contribution to a cell's transcriptome of Wnt pathway genes (activated by CHIR) across clusters as percent of transcriptome. FIG. 12B) Violin plot of expression contribution to a cell's transcriptome of Notch pathways genes (inhibited by DAPT) across clusters as percent of transcriptome. FIG. 12C) Violin plot of expression contribution to a cell's transcriptome of respiratory electron transport gene set across clusters as percent of transcriptome.

The figures herein are for illustrative purposes only and are not necessarily drawn to scale.

DETAILED DESCRIPTION OF THE EXAMPLE EMBODIMENTS General Definitions

Unless defined otherwise, technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this disclosure pertains. Definitions of common terms and techniques in molecular biology may be found in Molecular Cloning: A Laboratory Manual, 2^(nd) edition (1989) (Sambrook, Fritsch, and Maniatis); Molecular Cloning: A Laboratory Manual, 4^(th) edition (2012) (Green and Sambrook); Current Protocols in Molecular Biology (1987) (F. M. Ausubel et al. eds.); the series Methods in Enzymology (Academic Press, Inc.): PCR 2: A Practical Approach (1995) (M. J. MacPherson, B. D. Hames, and G. R. Taylor eds.): Antibodies, A Laboratory Manual (1988) (Harlow and Lane, eds.): Antibodies A Laboratory Manual, 2^(nd) edition 2013 (E. A. Greenfield ed.); Animal Cell Culture (1987) (R. I. Freshney, ed.); Benjamin Lewin, Genes IX, published by Jones and Bartlet, 2008 (ISBN 0763752223); Kendrew et al. (eds.), The Encyclopedia of Molecular Biology, published by Blackwell Science Ltd., 1994 (ISBN 0632021829); Robert A. Meyers (ed.), Molecular Biology and Biotechnology: a Comprehensive Desk Reference, published by VCH Publishers, Inc., 1995 (ISBN 9780471185710); Singleton et al., Dictionary of Microbiology and Molecular Biology 2nd ed., J. Wiley & Sons (New York, N.Y. 1994), March, Advanced Organic Chemistry Reactions, Mechanisms and Structure 4th ed., John Wiley & Sons (New York, N.Y. 1992); and Marten H. Hofker and Jan van Deursen, Transgenic Mouse Methods and Protocols, 2^(nd) edition (2011).

As used herein, the singular forms “a”, “an”, and “the” include both singular and plural referents unless the context clearly dictates otherwise.

The term “optional” or “optionally” means that the subsequent described event, circumstance or substituent may or may not occur, and that the description includes instances where the event or circumstance occurs and instances where it does not.

The recitation of numerical ranges by endpoints includes all numbers and fractions subsumed within the respective ranges, as well as the recited endpoints.

The terms “about” or “approximately” as used herein when referring to a measurable value such as a parameter, an amount, a temporal duration, and the like, are meant to encompass variations of and from the specified value, such as variations of +/−10% or less, +/−5% or less, +/−1% or less, and +/−0.1% or less of and from the specified value, insofar such variations are appropriate to perform in the disclosed invention. It is to be understood that the value to which the modifier “about” or “approximately” refers is itself also specifically, and preferably, disclosed.

As used herein, a “biological sample” may contain whole cells and/or live cells and/or cell debris. The biological sample may contain (or be derived from) a “bodily fluid”. The present invention encompasses embodiments wherein the bodily fluid is selected from amniotic fluid, aqueous humour, vitreous humour, bile, blood serum, breast milk, cerebrospinal fluid, cerumen (earwax), chyle, chyme, endolymph, perilymph, exudates, feces, female ejaculate, gastric acid, gastric juice, lymph, mucus (including nasal drainage and phlegm), pericardial fluid, peritoneal fluid, pleural fluid, pus, rheum, saliva, sebum (skin oil), semen, sputum, synovial fluid, sweat, tears, urine, vaginal secretion, vomit and mixtures of one or more thereof. Biological samples include cell cultures, bodily fluids, cell cultures from bodily fluids. Bodily fluids may be obtained from a mammal organism, for example by puncture, or other collecting or sampling procedures.

The terms “subject,” “individual,” and “patient” are used interchangeably herein to refer to a vertebrate, preferably a mammal, more preferably a human. Mammals include, but are not limited to, murines, simians, humans, farm animals, sport animals, and pets. Tissues, cells and their progeny of a biological entity obtained in vivo or cultured in vitro are also encompassed.

Various embodiments are described hereinafter. It should be noted that the specific embodiments are not intended as an exhaustive description or as a limitation to the broader aspects discussed herein. One aspect described in conjunction with a particular embodiment is not necessarily limited to that embodiment and can be practiced with any other embodiment(s). Reference throughout this specification to “one embodiment”, “an embodiment,” “an example embodiment,” means that a particular feature, structure or characteristic described in connection with the embodiment is included in at least one embodiment of the present invention. Thus, appearances of the phrases “in one embodiment,” “in an embodiment,” or “an example embodiment” in various places throughout this specification are not necessarily all referring to the same embodiment, but may. Furthermore, the particular features, structures or characteristics may be combined in any suitable manner, as would be apparent to a person skilled in the art from this disclosure, in one or more embodiments. Furthermore, while some embodiments described herein include some but not other features included in other embodiments, combinations of features of different embodiments are meant to be within the scope of the invention. For example, in the appended claims, any of the claimed embodiments can be used in any combination.

All publications, published patent documents, and patent applications cited herein are hereby incorporated by reference to the same extent as though each individual publication, published patent document, or patent application was specifically and individually indicated as being incorporated by reference.

Overview

Embodiments disclosed herein provide for ex vivo cell-based systems that faithfully recapitulate an in vivo phenotype of interest and methods of generating and using the cell-based systems. As used herein, to “recapitulate an in vivo phenotype” may include increasing the biological fidelity of an ex vivo cell-based system to more closely mimic the physiology and/or structure of a target in vivo system. Mimicking the physiology and/or structure of target in vivo system may comprise mimicking expression signatures or modules found in the target in vivo system, mimicking a cell state or states found in the target in vivo system, and/or mimicking the composition of cell types or sub-types found in the in vivo target system. Applicants provide for the first time a genome wide method of comparing ex vivo and in vitro systems to in vivo systems to identify specific pathways and genes for modulation to obtain cells that more faithfully recapitulate the in vivo system's phenotype of interest. Thus, the method provides for an unbiased global comparison of whole transcriptomes that does not prioritize previously identified markers. Previous studies compared specific cell type markers and concluded that in vitro cells recapitulated the in vivo cells based only on these on expression of these cell-specific markers (See e.g., International Patent Publication WO 2014/159356A1). An “ex vivo cell-based system” may comprise single cells of a particular type, sub-type or state, or a combination of cells of the same or differing type, sub-type, or state. The ex vivo cell-based system may be a model for screening perturbations to better understand the underlying biology or to identify putative targets for treating a disease, or for screening putative therapeutics, and also include models derived ex vivo but further implanted into a living organism, such as a mouse or pig, prior to perturbation of the model. An ex vivo cell-based system may also be a cell-based therapeutic for delivery to an organism to treat disease, or an implant meant to restore or regenerate damaged tissue. An “in vivo system” may likewise comprise a single cell or a combination of cells of the same or differing type, sub-type, or state. As used herein ex vivo may include, but not be limited to, in vitro systems, unless otherwise specifically indicated. The “in vivo system” may comprise healthy tissue or cells, or tissues or cells in a homeostatic state, or diseased tissue or cells, or diseased tissue or cells in a non-homeostatic state, or tissues or cells within a viable organism, or diseased tissue or cells within a viable organism. A homeostatic state may include cells or tissues demonstrating a physiology and/or structure typically observed in an healthy living organism. In other embodiments, a homeostatic state may be considered the state that a cell or tissue naturally adopts under a given set of growth conditions and absent further defined genetic, chemical, or environmental perturbations.

Current in vitro models used to look at biology are not well characterized with reference to in vivo models. The embodiments disclosed herein provide a means for identifying differences in expression at a single cell level and use this information to prioritize how to improve the ex vivo system to more faithfully recapitulate the biological characteristics of the target in vivo system. Particular advantageous uses for ex vivo cell-based systems that faithfully recapitulate an in vivo phenotype of interest include methods for identifying agents capable of inducing or suppressing certain gene signatures or gene expression modules and/or inducing or suppressing certain cell states in the ex vivo cell-based systems. In the context of cell-based therapeutics, the methods disclosed herein may also be used to design ex vivo cell-based systems that based on their programmed gene expression profile or configured cell state can either induce or suppress particular in vivo cell (sub)populations at the site of delivery. In another aspect, the methods disclosed herein provide a method for preparing cell-based therapeutics.

In certain example embodiments, a method for generating an ex vivo cell-based system that faithfully recapitulates an in vivo phenotype or target system of interest comprises first determining, using single cell RNA sequencing (scRNA-seq) one or more cell (sub)types or one or more cell states in an initial or starting ex vivo cell-based system. It should be noted that the methods disclosed herein may be used to develop an ex vivo cell-based system de novo from a source starting material, or to improve an existing ex vivo cell-based system. Source starting materials may include cultured cell lines or cells or tissues isolated directly from an in vivo source, including explants and biopsies. The source materials may be pluripotent cells including stem cells. Next, differences are identified in the cell (sub)type(s) and/or cell state(s) between the ex vivo cell-based systems a target in vivo system. The cell (sub)type(s) and cell state(s) of the in vivo system may likewise be determined using scRNA-seq. The scRNA-seq analysis may be obtained at the time of running the methods described herein are based on previously archived scRNA-seq analysis. Based on the identified differences, steps to modulate the source material to induce a shift in cell (sub)type(s) and/or cell state(s) that may more closely mimics the target in vivo system may then selected and applied.

In certain embodiments, different methods of single sequencing are better suited for sequencing certain samples (e.g., neurons, rare samples may be more optimally sequenced with a plate based method or single nuclei sequencing). In certain embodiments, the invention involves plate based single cell RNA sequencing (see, e.g., Picelli, S. et al., 2014, “Full-length RNA-seq from single cells using Smart-seq2” Nature protocols 9, 171-181, doi:10.1038/nprot.2014.006).

In certain embodiments, the invention involves high-throughput single-cell RNA-seq and/or targeted nucleic acid profiling (for example, sequencing, quantitative reverse transcription polymerase chain reaction, and the like) where the RNAs from different cells are tagged individually, allowing a single library to be created while retaining the cell identity of each read. In this regard reference is made to Macosko et al., 2015, “Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets” Cell 161, 1202-1214; International patent application number PCT/US2015/049178, published as WO2016/040476 on Mar. 17, 2016; Klein et al., 2015, “Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells” Cell 161, 1187-1201; International patent application number PCT/US2016/027734, published as WO2016168584A1 on Oct. 20, 2016; Zheng, et al., 2016, “Haplotyping germline and cancer genomes with high-throughput linked-read sequencing” Nature Biotechnology 34, 303-311; Zheng, et al., 2017, “Massively parallel digital transcriptional profiling of single cells” Nat. Commun. 8, 14049 doi: 10.1038/ncomms14049; International patent publication number WO 2014210353 A2; Zilionis, et al., 2017, “Single-cell barcoding and sequencing using droplet microfluidics” Nat Protoc. January; 12(1):44-73; Cao et al., 2017, “Comprehensive single cell transcriptional profiling of a multicellular organism by combinatorial indexing” bioRxiv preprint first posted online Feb. 2, 2017, doi: dx.doi.org/10.1101/104844; Rosenberg et al., 2017, “Scaling single cell transcriptomics through split pool barcoding” bioRxiv preprint first posted online Feb. 2, 2017, doi: dx.doi.org/10.1101/105163; Vitak, et al., “Sequencing thousands of single-cell genomes with combinatorial indexing” Nature Methods, 14(3):302-308, 2017; Cao, et al., Comprehensive single-cell transcriptional profiling of a multicellular organism. Science, 357(6352):661-667, 2017; and Gierahn et al., “Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput” Nature Methods 14, 395-398 (2017), all the contents and disclosure of each of which are herein incorporated by reference in their entirety.

In certain embodiments, the invention involves single nucleus RNA sequencing. In this regard reference is made to Swiech et al., 2014, “In vivo interrogation of gene function in the mammalian brain using CRISPR-Cas9” Nature Biotechnology Vol. 33, pp. 102-106; Habib et al., 2016, “Div-Seq: Single-nucleus RNA-Seq reveals dynamics of rare adult newborn neurons” Science, Vol. 353, Issue 6302, pp. 925-928; Habib et al., 2017, “Massively parallel single-nucleus RNA-seq with DroNc-seq” Nat Methods. 2017 October; 14(10):955-958; and International patent application number PCT/US2016/059239, published as WO2017164936 on Sep. 28, 2017, which are herein incorporated by reference in their entirety.

In certain example embodiments, assessing the cell (sub)types and states present in the in vivo system may comprise analysis of expression matrices from the scRNA-seq data, performing dimensionality reduction, graph-based clustering and deriving list of cluster-specific genes in order to identify cell types and/or states present in the in vivo system. These marker genes may then be used throughout to relate the ex vivo system cell (sub)types and states to the in vivo system. The same analysis may then be applied to the source material for the ex vivo cell-based system. From both sets of sc-RNAseq analysis an initial distribution of gene expression data is obtained. In certain embodiments, the distribution may be a count-based metric for the number of transcripts of each gene present in a cell. Further the clustering and gene expression matrix analysis allow for the identification of key genes in the initial ex vivo system and the target in vivo system, such as differences in the expression of key transcription factors. In certain example embodiments, this may be done conducting differential expression analysis. For example, in the Working Examples below, differential gene expression analysis identified that in vivo PCs were enriched in defensins and antimicrobials including Defa22, Defa21, Zg16, Ang4, Defa3, and Lyz1. At the same time the analysis revealed that the in vitro organoid-derived PC cells had a global reduction in the total number of organoid derived cells producing the identified PC marker set. Thus, the methods disclosed herein can both identify key markers of the target in vivo system and potential targets for modulation to shift the expression distribution of the ex vivo system towards that of the target in vivo system. Again turning to the PC example provided herein, the single-cell transcriptomic steps of the methods disclosed herein were used to identify that the in vivo PC cells were enriched in Wnt-targeted genes relative to in vitro PCs, accordingly modulation of Wnt and inhibition of Notch were selected to shift the expression profile of the in vitro PCs to that of the in vivo PCs.

Other methods for assessing differences in the ex vivo and in vivo systems may be employed. In certain example embodiments, an assessment of differences in the in vivo and ex vivo proteome may be used to further identify key differences in cell type and sub-types or cells. states. For example isobaric mass tag labeling and liquid chromatography mass spectroscopy may used to determine relative protein abundances in the ex vivo and in vivo systems. The working examples below provide further disclosure on leveraging proteome analysis within the context of the methods disclosed herein.

In certain example embodiments, a statistically significant shift in the initial ex vivo gene expression distribution toward the gene expression distribution of the in vivo systems is sought post-modulation. A statistically significant shift in gene expression distribution can be at least 10%, at least 11%, at least 12%, at least 13%, at least 14%, at least 15%, at least 20%, at least 21%, at least 22%, at least 23%, at least 24%, at least 25%, at least 26%, at least 27%, at least 28%, at least 29%, at least 30%, at least 31%, at least 32%, at least 33%, at least 34%, at least 35%, at least 36%, at least 37%, at least 38%, at least 39%, at least 40%, at least 41%, at least 42%, at least 43%, at least 44%, at least 45%, at least 46%, at least 47%, at least 48%, at least 49%, at least 50%, at least 51%, at least 52%, at least 53%, at least 54%, at least 55%, at least 56%, at least 57%, at least 58%, at least 59%, at least 60%, at least 61%, at least 62%, at least 63%, at least 64%, at least 65%, at least 66%, at least 67%, at least 68%, at least 69%, at least 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99%.

In certain example embodiments, statistical shifts may be determined by defining an in vivo score. For example, a gene list of key genes enriched in the in vivo model may be defined. To determine the fractional contribution to a cell's transcriptome to that gene list, the total log (scaled UMI+1) expression values for gene with the list of interest are summed and then divided by the total amount of scaled UMI detected in that cell giving a proportion of a cell's transcriptome dedicated to producing those genes. Thus, statistical significant shifts may be shifts in an initial score for the ex vivo system after modulation towards the in vivo score or after modulation with an aim of moving in a statistically significant fashion towards the in vivo score.

Modulation may be monitored in a number of ways. For example, expression of one or more key marker genes identified as described above may be measured at regular levels to assess increases in expression levels. Shifting of the ex vivo system to that of the in vivo system may also be measured phenotypically. For example, imaging an immunocytochemistry for key in vivo markers may be assessed at regular intervals to detect increased expression of the key in vivo markers. Likewise, flow cytometry may be used in a similar manner. In addition, to detecting key in vivo markers, imaging modalities such as those described above may be used to further detect changes in cell morphology of the ex vivo system to more closely resemble the target in vivo system.

In certain example embodiments, the ex vivo system may be further modulated to not only more faithfully recapitulate a target in vivo system, but the ex vivo system may be further modulated to induce a gain of function. For example, one or more genes, gene expression cassettes (modules), or gene expression signature associated with the gain of function may be induced. Example gain of functions include, but are not limited to, increased anti-apoptotic activity or improved anti-microbial secretion.

In certain embodiments, gene signatures are modulated to shift an ex vivo system to more faithfully recapitulate an in vivo system. As used herein a “signature” may encompass any gene or genes, protein or proteins, or epigenetic element(s) whose expression profile or whose occurrence is associated with a specific cell type, subtype, or cell state of a specific cell type or subtype within a population of cells. For ease of discussion, when discussing gene expression, any of gene or genes, protein or proteins, or epigenetic element(s) may be substituted. As used herein, the terms “signature”, “expression profile”, or “expression program” may be used interchangeably. It is to be understood that also when referring to proteins (e.g. differentially expressed proteins), such may fall within the definition of “gene” signature. Levels of expression or activity or prevalence may be compared between different cells in order to characterize or identify for instance signatures specific for cell (sub)populations. Increased or decreased expression or activity or prevalence of signature genes may be compared between different cells in order to characterize or identify for instance specific cell (sub)populations. The detection of a signature in single cells may be used to identify and quantitate for instance specific cell (sub)populations. A signature may include a gene or genes, protein or proteins, or epigenetic element(s) whose expression or occurrence is specific to a cell (sub)population, such that expression or occurrence is exclusive to the cell (sub)population. A gene signature as used herein, may thus refer to any set of up- and down-regulated genes that are representative of a cell type or subtype. A gene signature as used herein, may also refer to any set of up- and down-regulated genes between different cells or cell (sub)populations derived from a gene-expression profile. For example, a gene signature may comprise a list of genes differentially expressed in a distinction of interest.

The signature as defined herein (being it a gene signature, protein signature or other genetic or epigenetic signature) can be used to indicate the presence of a cell type, a subtype of the cell type, the state of the microenvironment of a population of cells, a particular cell type population or subpopulation, and/or the overall status of the entire cell (sub)population. Furthermore, the signature may be indicative of cells within a population of cells in vivo. The signature may also be used to suggest for instance particular therapies, or to follow up treatment, or to suggest ways to modulate immune systems. The signatures of the present invention may be discovered by analysis of expression profiles of single-cells within a population of cells from isolated samples (e.g. tumor samples), thus allowing the discovery of novel cell subtypes or cell states that were previously invisible or unrecognized. The presence of subtypes or cell states may be determined by subtype specific or cell state specific signatures. The presence of these specific cell (sub)types or cell states may be determined by applying the signature genes to bulk sequencing data in a sample. Not being bound by a theory the signatures of the present invention may be microenvironment specific, such as their expression in a particular spatio-temporal context. Not being bound by a theory, signatures as discussed herein are specific to a particular pathological context. Not being bound by a theory, a combination of cell subtypes having a particular signature may indicate an outcome. Not being bound by a theory, the signatures can be used to deconvolute the network of cells present in a particular pathological condition. Not being bound by a theory the presence of specific cells and cell subtypes are indicative of a particular response to treatment, such as including increased or decreased susceptibility to treatment. The signature may indicate the presence of one particular cell type. In one embodiment, the novel signatures are used to detect multiple cell states or hierarchies that occur in subpopulations of cancer cells that are linked to particular pathological condition (e.g. cancer grade), or linked to a particular outcome or progression of the disease (e.g. metastasis), or linked to a particular response to treatment of the disease.

The signature according to certain embodiments of the present invention may comprise or consist of one or more genes, proteins and/or epigenetic elements, such as for instance 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more. In certain embodiments, the signature may comprise or consist of two or more genes, proteins and/or epigenetic elements, such as for instance 2, 3, 4, 5, 6, 7, 8, 9, 10 or more. In certain embodiments, the signature may comprise or consist of three or more genes, proteins and/or epigenetic elements, such as for instance 3, 4, 5, 6, 7, 8, 9, 10 or more. In certain embodiments, the signature may comprise or consist of four or more genes, proteins and/or epigenetic elements, such as for instance 4, 5, 6, 7, 8, 9, 10 or more. In certain embodiments, the signature may comprise or consist of five or more genes, proteins and/or epigenetic elements, such as for instance 5, 6, 7, 8, 9, 10 or more. In certain embodiments, the signature may comprise or consist of six or more genes, proteins and/or epigenetic elements, such as for instance 6, 7, 8, 9, 10 or more. In certain embodiments, the signature may comprise or consist of seven or more genes, proteins and/or epigenetic elements, such as for instance 7, 8, 9, 10 or more. In certain embodiments, the signature may comprise or consist of eight or more genes, proteins and/or epigenetic elements, such as for instance 8, 9, 10 or more. In certain embodiments, the signature may comprise or consist of nine or more genes, proteins and/or epigenetic elements, such as for instance 9, 10 or more. In certain embodiments, the signature may comprise or consist of ten or more genes, proteins and/or epigenetic elements, such as for instance 10, 11, 12, 13, 14, 15, or more. It is to be understood that a signature according to the invention may for instance also include genes or proteins as well as epigenetic elements combined.

In certain embodiments, a signature is characterized as being specific for a particular cell or cell (sub)population if it is upregulated or only present, detected or detectable in that particular cell or cell (sub)population, or alternatively is downregulated or only absent, or undetectable in that particular cell or cell (sub)population. In this context, a signature consists of one or more differentially expressed genes/proteins or differential epigenetic elements when comparing different cells or cell (sub)populations, including comparing different tumor cells or tumor cell (sub)populations, as well as comparing tumor cells or tumor cell (sub)populations with non-tumor cells or non-tumor cell (sub)populations. It is to be understood that “differentially expressed” genes/proteins include genes/proteins which are up- or down-regulated as well as genes/proteins which are turned on or off. When referring to up-or down-regulation, in certain embodiments, such up- or down-regulation is preferably at least two-fold, such as two-fold, three-fold, four-fold, five-fold, or more, such as for instance at least ten-fold, at least 20-fold, at least 30-fold, at least 40-fold, at least 50-fold, or more. Alternatively, or in addition, differential expression may be determined based on common statistical tests, as is known in the art.

As discussed herein, differentially expressed genes/proteins, or differential epigenetic elements may be differentially expressed on a single cell level, or may be differentially expressed on a cell population level. Preferably, the differentially expressed genes/proteins or epigenetic elements as discussed herein, such as constituting the gene signatures as discussed herein, when as to the cell population level, refer to genes that are differentially expressed in all or substantially all cells of the population (such as at least 80%, preferably at least 90%, such as at least 95% of the individual cells). This allows one to define a particular subpopulation of cells. As referred to herein, a “subpopulation” of cells preferably refers to a particular subset of cells of a particular cell type which can be distinguished or are uniquely identifiable and set apart from other cells of this cell type. The cell subpopulation may be phenotypically characterized, and is preferably characterized by the signature as discussed herein. A cell (sub)population as referred to herein may constitute of a (sub)population of cells of a particular cell type characterized by a specific cell state.

When referring to induction, or alternatively suppression of a particular signature, preferable is meant induction or alternatively suppression (or upregulation or downregulation) of at least one gene/protein and/or epigenetic element of the signature, such as for instance at least to, at least three, at least four, at least five, at least six, or all genes/proteins and/or epigenetic elements of the signature.

In further aspects, the invention relates to gene signatures, protein signature, and/or other genetic or epigenetic signature of particular tumor cell subpopulations, as defined herein elsewhere. The invention hereto also further relates to particular tumor cell subpopulations, which may be identified based on the methods according to the invention as discussed herein; as well as methods to obtain such cell (sub)populations and screening methods to identify agents capable of inducing or suppressing particular tumor cell (sub)populations.

Modulating Agents

Selection of modulating agents will depend on key targets identified by the analysis describe above, and which aspects of gene expression need to be modified to shift expression towards that of the in vivo model. Modulating agents may comprise cytokines, growth factors, hormones, transcription factors, metabolites or small molecules. The modulating agent may also be a genetic modifying agent or an epigenetic modifying agent. The genetic modulating agent may be a CRISPR system, a zinc finger nuclease system, a TALEN, or a meganuclease. The epigenetic modifying agent may be a DNA methylation inhibitor, HDAC inhibitor, histone acetylation inhibitor, histone methylation inhibitor, or histone demethylase inhibitor.

Ex Vivo Cell Culture

In certain embodiments, the ex vivo cell-based system comprises a single cell type or sub-type, a combination of cell types and/or subtypes, cell-based therapeutic, an explant, or an organoid derived using the methods disclosed herein.

In certain embodiments, the single cell type or subtype or combination of cell types and/or subtypes comprises an immune cell, intestinal cell, liver cell, kidney cell, lung cell, brain cell, epithelial cell, endoderm cell, neuron, ectoderm cell, islet cell, acinar cell, oocyte, sperm, hematopoietic cell, hepatocyte, ski n/keratinocyte, melan ocyte, bone/osteocyte, hair/dermal papilla cell, cartilage/chondrocyte, fat cell/adipocyte, skeletal muscular cell, endothelium cell, cardiac muscle/cardiomyocyte, trophoblast, tumor cell, or tumor microenvironment (TME) cell.

In certain embodiments, the single cell type or sub-type is pluripotent, or the combination of cell types and/or subtypes comprises one or more stem cells. The one or more stem cells may be selected from the group consisting of lymphoid stem cells, myeloid stem cells, neural stem cells, skeletal muscle satellite cells, epithelial stem cells, endodermal and neuroectodermal stem cells, germ cells, extraembryonic and embryonic stem cells, mesenchymal stem cells, intestinal stem cells, embryonic stem cells, and induced pluripotent stem cells (iPSCs).

As used herein, the term “stem cell” refers to a multipotent cell having the capacity to self-renew and to differentiate into multiple cell lineages.

As used herein, the term “epithelial stem cell” refers to a multipotent cell which has the potential to become committed to multiple cell lineages, including cell lineages resulting in epithelial cells.

The tumor microenvironment (TME) is the cellular environment in which the tumor exists, including surrounding blood vessels, immune cells, cancer associated fibroblasts (CAFs), bone marrow-derived inflammatory cells, lymphocytes, signaling molecules and the extracellular matrix (ECM).

Tumor infiltrating lymphocytes (TILs) are lymphocytes that penetrate a tumor.

In certain embodiments, a cell-based therapeutic includes engraftment of the cells of the present invention. As used herein, the term “engraft” or “engraftment” refers to the process of cell incorporation into a tissue of interest in vivo through contact with existing cells of the tissue.

As used herein, a “population” of cells is any number of cells greater than 1, but is preferably at least 1×10³ cells, at least 1×10⁴ cells, at least at least 1×10⁵ cells, at least 1×10⁶ cells, at least 1×10⁷ cells, at least 1×10⁸ cells, at least 1×10⁹ cells, or at least 1×10¹⁰ cells.

As used herein, the term “organoid” or “epithelial organoid” refers to a cell cluster or aggregate that resembles an organ, or part of an organ, and possesses cell types relevant to that particular organ.

As used herein, a “subject” is a vertebrate, including any member of the class mammalia.

As used herein, a “mammal” refers to any mammal including but not limited to human, mouse, rat, sheep, monkey, goat, rabbit, hamster, horse, cow or pig.

A “non-human mammal”, as used herein, refers to any mammal that is not a human.

General techniques useful in the practice of this invention in cell culture and media uses are known in the art (e.g., Large Scale Mammalian Cell Culture (Hu et al. 1997. Curr Opin Biotechnol 8: 148); Serum-free Media (K. Kitano. 1991. Biotechnology 17: 73); or Large Scale Mammalian Cell Culture (Curr Opin Biotechnol 2: 375, 1991). The terms “culturing” or “cell culture” are common in the art and broadly refer to maintenance of cells and potentially expansion (proliferation, propagation) of cells in vitro. Typically, animal cells, such as mammalian cells, such as human cells, are cultured by exposing them to (i.e., contacting them with) a suitable cell culture medium in a vessel or container adequate for the purpose (e.g., a 96-, 24-, or 6-well plate, a T-25, T-75, T-150 or T-225 flask, or a cell factory), at art-known conditions conducive to in vitro cell culture, such as temperature of 37° C., 5% v/v CO₂ and >95% humidity.

Methods related to stem cells and differentiating stem cells are known in the art (see, e.g., “Teratocarcinomas and embryonic stem cells: A practical approach” (E. J. Robertson, ed., IRL Press Ltd. 1987); “Guide to Techniques in Mouse Development” (P. M. Wasserman et al. eds., Academic Press 1993); “Embryonic Stem Cells: Methods and Protocols” (Kursad Turksen, ed., Humana Press, Totowa N.J., 2001); “Embryonic Stem Cell Differentiation in Vitro” (M. V. Wiles, Meth. Enzymol. 225: 900, 1993); “Properties and uses of Embryonic Stem Cells: Prospects for Application to Human Biology and Gene Therapy” (P. D. Rathjen et al., al., 1993). Differentiation of stem cells is reviewed, e.g., in Robertson. 1997. Meth Cell Biol 75: 173; Roach and McNeish. 2002. Methods Mol Biol 185: 1-16; and Pedersen. 1998. Reprod Fertil Dev 10: 31). For further elaboration of general techniques useful in the practice of this invention, the practitioner can refer to standard textbooks and reviews in cell biology, tissue culture, and embryology (see, e.g., Culture of Human Stem Cells (R. Ian Freshney, Glyn N. Stacey, Jonathan M. Auerbach—2007); Protocols for Neural Cell Culture (Laurie C. Doering—2009); Neural Stem Cell Assays (Navjot Kaur, Mohan C. Vemuri—2015); Working with Stem Cells (Henning Ulrich, Priscilla Davidson Negraes—2016); and Biomaterials as Stem Cell Niche (Krishnendu Roy—2010)).

Organoid technology has been previously described for example, for brain, retinal, stomach, lung, thyroid, small intestine, colon, liver, kidney, pancreas, prostate, mammary gland, fallopian tube, taste buds, salivary glands, and esophagus (see, e.g., Clevers, Modeling Development and Disease with Organoids, Cell. 2016 Jun. 16; 165(7):1586-1597).

For further methods of cell culture solutions and systems, see International Patent publication WO2014159356A1.

In certain embodiments, modulating the ex vivo cell-based system comprises delivering one or more modulating agents that modify expression of one or more cell types or states in the ex vivo cell-based system, delivering an additional cell type or sub-type to the ex vivo cell-based system, or depleting an existing cell type or sub-type from the ex vivo cell-based system. The one or more modulating agents may comprise one or more cytokines, growth factors, hormones, transcription factors, metabolites or small molecules.

The term “modulate” broadly denotes a qualitative and/or quantitative alteration, change or variation in that which is being modulated. Where modulation can be assessed quantitatively—for example, where modulation comprises or consists of a change in a quantifiable variable such as a quantifiable property of a cell or where a quantifiable variable provides a suitable surrogate for the modulation—modulation specifically encompasses both increase (e.g., activation) or decrease (e.g., inhibition) in the measured variable. The term encompasses any extent of such modulation, e.g., any extent of such increase or decrease, and may more particularly refer to statistically significant increase or decrease in the measured variable. By means of example, modulation may encompass an increase in the value of the measured variable by at least about 10%, e.g., by at least about 20%, preferably by at least about 30%, e.g., by at least about 40%, more preferably by at least about 50%, e.g., by at least about 75%, even more preferably by at least about 100%, e.g., by at least about 150%, 200%, 250%, 300%, 400% or by at least about 500%, compared to a reference situation without said modulation; or modulation may encompass a decrease or reduction in the value of the measured variable by at least about 10%, e.g., by at least about 20%, by at least about 30%, e.g., by at least about 40%, by at least about 50%, e.g., by at least about 60%, by at least about 70%, e.g., by at least about 80%, by at least about 90%, e.g., by at least about 95%, such as by at least about 96%, 97%, 98%, 99% or even by 100%, compared to a reference situation without said modulation. Preferably, modulation may be specific or selective, hence, one or more desired phenotypic aspects of a cell or cell population may be modulated without substantially altering other (unintended, undesired) phenotypic aspect(s).

Non-limiting examples of hormones include growth hormone (GH), adrenocorticotropic hormone (ACTH), dehydroepiandrosterone (DHEA), cortisol, epinephrine, thyroid hormone, estrogen, progesterone, testosterone, or combinations thereof.

Non-limiting examples of cytokines include lymphokines (e.g., interferon-γ, IL-2, IL-3, IL-4, IL-6, granulocyte-macrophage colony-stimulating factor (GM-CSF), interferon-γ, leukocyte migration inhibitory factors (T-LIF, B-LIF), lymphotoxin-alpha, macrophage-activating factor (MAF), macrophage migration-inhibitory factor (MIF), neuroleukin, immunologic suppressor factors, transfer factors, or combinations thereof), monokines (e.g., IL-1, TNF-alpha, interferon-α, interferon-β, colony stimulating factors, e.g., CSF2, CSF3, macrophage CSF or GM-CSF, or combinations thereof), chemokines (e.g., beta-thromboglobulin, C chemokines, CC chemokines, CXC chemokines, CX3C chemokines, macrophage inflammatory protein (MIP), or combinations thereof), interleukins (e.g., IL-1, IL-2, IL-3, IL-4, IL-5, IL-6, IL-7, IL-8, IL-9, IL-10, IL-11, IL-12, IL-13, IL-14, IL-15, IL-17, IL-18, IL-19, IL-20, IL-21, IL-22, IL-23, IL-24, IL-25, IL-26, IL-27, IL-28, IL-29, IL-30, IL-31, IL-32, IL-33, IL-34, IL-35, IL-36, or combinations thereof), and several related signalling molecules, such as tumour necrosis factor (TNF) and interferons (e.g., interferon-α, interferon-β, interferon-γ, interferon-λ, or combinations thereof).

Non-limiting examples of growth factors include those of fibroblast growth factor (FGF) family, bone morphogenic protein (BMP) family, platelet derived growth factor (PDGF) family, transforming growth factor beta (TGFbeta) family, nerve growth factor (NGF) family, epidermal growth factor (EGF) family, insulin related growth factor (IGF) family, hepatocyte growth factor (HGF) family, hematopoietic growth factors (HeGFs), platelet-derived endothelial cell growth factor (PD-ECGF), angiopoietin, vascular endothelial growth factor (VEGF) family, glucocorticoids, or combinations thereof.

Non-limiting examples of mitogens include phytohaemagglutinin (PHA), concanavalin A (conA), lipopolysaccharide (LPS), pokeweed mitogen (PWM), phorbol ester such as phorbol myristate acetate (PMA) with or without ionomycin, or combinations thereof.

Non-limiting examples of cell surface receptors the ligands of which may act as immunomodulants include Toll-like receptors (TLRs) (e.g., TLR1, TLR2, TLR3, TLR4, TLR5, TLR6, TLR7, TLR8, TLR9, TLR10, TLR11, TLR12 or TLR13), CD80, CD86, CD40, CCR7, or C-type lectin receptors.

In certain embodiments, differentiation promoting agents may be used to obtain particular types of target cells. Differentiation promoting agents include anticoagulants, chelating agents, and antibiotics. Examples of such agents may be one or more of the following: vitamins and minerals or derivatives thereof, such as A (retinol), B₃, C (ascorbate), ascorbate 2-phosphate, D such as D₂ or D₃, K, retinoic acid, nicotinamide, zinc or zinc compound, and calcium or calcium compounds; natural or synthetic hormones such as hydrocortisone, and dexamethasone; amino acids or derivatives thereof, such as L-glutamine (L-glu), ethylene glycol tetracetic acid (EGTA), proline, and non-essential amino acids (NEAA); compounds or derivatives thereof, such as 3-mercaptoethal, dibutyl cyclic adenosine monophosphate (db-cAMP), monothioglycerol (MTG), putrescine, dimethyl sulfoxide (DMSO), hypoxanthine, adenine, forskolin, cilostamide, and 3-isobutyl-1-methylxanthine; nucleosides and analogues thereof, such as 5-azacytidine; acids or salts thereof, such as ascorbic acid, pyruvate, okadic acid, linoleic acid, ethylenediaminetetraacetic acid (EDTA), anticoagulant citrate dextrose formula A (ACDA), disodium EDTA, sodium butyrate, and glycerophosphate; antibiotics or drugs, such as G418, gentamycine, Pentoxifylline (1-(5-oxohexyl)-3,7-dimethylxanthine), and indomethacin; and proteins such as tissue plasminogen activator (TPA).

Adoptive Cell Transfer

In certain embodiments, the cell based therapy may comprise adoptive cell transfer (ACT). The ex vivo cell-based system that is modulated to faithfully recapitulate an in vivo system may be transferred to a subject in need thereof. The cell based therapy may comprise adoptive cell transfer (ACT) of T cells. The T cells may be activated or effector T cells specific for a tumor antigen. The T cells may be further modified as described herein.

In certain embodiments, cells as described herein and below may be used for adoptive cell transfer (ACT). ACT as used herein also refers to adoptive cell transfer. As used herein adoptive cell transfer and adoptive cell therapy are used interchangeably. In certain embodiments, the interaction of immune cells is advantageously used, such as modulating and/or transferring one immune cell subtype to cause an effect in another immune cell subtype. The transferred cells may include and be modulated by immune cells or immune cell populations as taught herein. In certain embodiments, the suppressive T cells of the present invention are depleted from cells used in ACT and may be transferred to a subject suffering from a disease (e.g., cancer). In certain embodiments, the cells of the present invention may be transferred to a subject suffering from a disease characteristic of an over reactive immune response (e.g., autoimmune disease). In certain embodiments, adoptive cell transfer may comprise: isolating from a biological sample of the subject a CD4+ and/or CD8⁺ T cell or CD4+ and/or CD8⁺ T cell population as described herein; in vitro expanding the T cell or T cell population; and administering the in vitro expanded T cell or T cell population to the subject. The method may further comprise enriching the expanded T cells for one subtype. In certain embodiments, the method may further comprise formulating the in vitro expanded immune cell or immune cell population into a pharmaceutical composition.

In certain embodiments, the present invention comprises adoptive cell therapy. Adoptive cell therapy can refer to the transfer of cells, most commonly immune-derived cells, back into the same patient or into a new recipient host with the goal of transferring the immunologic functionality and characteristics into the new host. If possible, use of autologous cells helps the recipient by minimizing GVHD issues. The adoptive transfer of autologous tumor infiltrating lymphocytes (TIL) (Besser et al., (2010) Clin. Cancer Res 16 (9) 2646-55; Dudley et al., (2002) Science 298 (5594): 850-4; and Dudley et al., (2005) Journal of Clinical Oncology 23 (10): 2346-57.) or genetically re-directed peripheral blood mononuclear cells (Johnson et al., (2009) Blood 114 (3): 535-46; and Morgan et al., (2006) Science 314(5796) 126-9) has been used to successfully treat patients with advanced solid tumors, including melanoma and colorectal carcinoma, as well as patients with CD19-expressing hematologic malignancies (Kalos et al., (2011) Science Translational Medicine 3 (95): 95ra73).

Aspects of the invention involve the adoptive transfer of immune system cells, such as T cells, specific for selected antigens, such as tumor associated antigens or tumor specific neoantigens (see Maus et al., 2014, Adoptive Immunotherapy for Cancer or Viruses, Annual Review of Immunology, Vol. 32: 189-225; Rosenberg and Restifo, 2015, Adoptive cell transfer as personalized immunotherapy for human cancer, Science Vol. 348 no. 6230 pp. 62-68; Restifo et al., 2015, Adoptive immunotherapy for cancer: harnessing the T cell response. Nat. Rev. Immunol. 12(4): 269-281; and Jenson and Riddell, 2014, Design and implementation of adoptive therapy with chimeric antigen receptor-modified T cells. Immunol Rev. 257(1): 127-144; and Rajasagi et al., 2014, Systematic identification of personal tumor-specific neoantigens in chronic lymphocytic leukemia. Blood. 2014 Jul. 17; 124(3):453-62).

In certain embodiments, an antigen (such as a tumor antigen) to be targeted in adoptive cell therapy (such as particularly CAR or TCR T-cell therapy) of a disease (such as particularly of tumor or cancer) may be selected from a group consisting of: B cell maturation antigen (BCMA); PSA (prostate-specific antigen); prostate-specific membrane antigen (PSMA); PSCA (Prostate stem cell antigen); Tyrosine-protein kinase transmembrane receptor ROR1; fibroblast activation protein (FAP); Tumor-associated glycoprotein 72 (TAG72); Carcinoembryonic antigen (CEA); Epithelial cell adhesion molecule (EPCAM); Mesothelin; Human Epidermal growth factor Receptor 2 (ERBB2 (Her2/neu)); Prostase; Prostatic acid phosphatase (PAP); elongation factor 2 mutant (ELF2M); Insulin-like growth factor 1 receptor (IGF-1R); gplOO; BCR-ABL (breakpoint cluster region-Abelson); tyrosinase; New York esophageal squamous cell carcinoma 1 (NY-ESO-1); K-light chain, LAGE (L antigen); MAGE (melanoma antigen); Melanoma-associated antigen 1 (MAGE-A1); MAGE A3; MAGE A6; legumain; Human papillomavirus (HPV) E6; HPV E7; prostein; survivin; PCTA1 (Galectin 8); Melan-A/MART-1; Ras mutant; TRP-1 (tyrosinase related protein 1, or gp75); Tyrosinase-related Protein 2 (TRP2); TRP-2/INT2 (TRP-2/intron 2); RAGE (renal antigen); receptor for advanced glycation end products 1 (RAGE1); Renal ubiquitous 1, 2 (RU1, RU2); intestinal carboxyl esterase (iCE); Heat shock protein 70-2 (HSP70-2) mutant; thyroid stimulating hormone receptor (TSHR); CD123; CD171; CD19; CD20; CD22; CD26; CD30; CD33; CD44v7/8 (cluster of differentiation 44, exons 7/8); CD53; CD92; CD100; CD148; CD150; CD200; CD261; CD262; CD362; CS-1 (CD2 subset 1, CRACC, SLAMF7, CD319, and 19A24); C-type lectin-like molecule-1 (CLL-1); ganglioside GD3 (aNeu5Ac(2-8)aNeu5Ac(2-3)bDGalp(1-4)bDGlcp(1-1)Cer); Tn antigen (Tn Ag); Fms-Like Tyrosine Kinase 3 (FLT3); CD38; CD138; CD44v6; B7H3 (CD276); KIT (CD117); Interleukin-13 receptor subunit alpha-2 (IL-13Ra2); Interleukin 11 receptor alpha (IL-11Ra); prostate stem cell antigen (PSCA); Protease Serine 21 (PRSS21); vascular endothelial growth factor receptor 2 (VEGFR2); Lewis(Y) antigen; CD24; Platelet-derived growth factor receptor beta (PDGFR-beta); stage-specific embryonic antigen-4 (SSEA-4); Mucin 1, cell surface associated (MUC1); mucin 16 (MUC16); epidermal growth factor receptor (EGFR); epidermal growth factor receptor variant III (EGFRvIII); neural cell adhesion molecule (NCAM); carbonic anhydrase IX (CAIX); Proteasome (Prosome, Macropain) Subunit, Beta Type, 9 (LMP2); ephrin type-A receptor 2 (EphA2); Ephrin B2; Fucosyl GM1; sialyl Lewis adhesion molecule (sLe); ganglioside GM3 (aNeu5Ac(2-3)bDGalp(1-4)bDGlcp(1-1)Cer); TGS5; high molecular weight-melanoma-associated antigen (HMWMAA); o-acetyl-GD2 ganglioside (OAcGD2); Folate receptor alpha; Folate receptor beta; tumor endothelial marker 1 (TEM1/CD248); tumor endothelial marker 7-related (TEM7R); claudin 6 (CLDN6); G protein-coupled receptor class C group 5, member D (GPRC5D); chromosome X open reading frame 61 (CXORF61); CD97; CD179a; anaplastic lymphoma kinase (ALK); Polysialic acid; placenta-specific 1 (PLAC1); hexasaccharide portion of globoH glycoceramide (GloboH); mammary gland differentiation antigen (NY-BR-1); uroplakin 2 (UPK2); Hepatitis A virus cellular receptor 1 (HAVCR1); adrenoceptor beta 3 (ADRB3); pannexin 3 (PANX3); G protein-coupled receptor 20 (GPR20); lymphocyte antigen 6 complex, locus K 9 (LY6K); Olfactory receptor 51E2 (OR51E2); TCR Gamma Alternate Reading Frame Protein (TARP); Wilms tumor protein (WT1); ETS translocation-variant gene 6, located on chromosome 12p (ETV6-AML); sperm protein 17 (SPA17); X Antigen Family, Member 1A (XAGE1); angiopoietin-binding cell surface receptor 2 (Tie 2); CT (cancer/testis (antigen)); melanoma cancer testis antigen-1 (MAD-CT-1); melanoma cancer testis antigen-2 (MAD-CT-2); Fos-related antigen 1; p53; p53 mutant; human Telomerase reverse transcriptase (hTERT); sarcoma translocation breakpoints; melanoma inhibitor of apoptosis (ML-IAP); ERG (transmembrane protease, serine 2 (TMPRSS2) ETS fusion gene); N-Acetyl glucosaminyl-transferase V (NA17); paired box protein Pax-3 (PAX3); Androgen receptor; Cyclin B1; Cyclin D1; v-myc avian myelocytomatosis viral oncogene neuroblastoma derived homolog (MYCN); Ras Homolog Family Member C (RhoC); Cytochrome P450 1B1 (CYP1B1); CCCTC-Binding Factor (Zinc Finger Protein)-Like (BORIS); Squamous Cell Carcinoma Antigen Recognized By T Cells-1 or 3 (SART1, SART3); Paired box protein Pax-5 (PAX5); proacrosin binding protein sp32 (OY-TES1); lymphocyte-specific protein tyrosine kinase (LCK); A kinase anchor protein 4 (AKAP-4); synovial sarcoma, X breakpoint-1, -2, -3 or -4 (SSX1, SSX2, SSX3, SSX4); CD79a; CD79b; CD72; Leukocyte-associated immunoglobulin-like receptor 1 (LAIR1); Fc fragment of IgA receptor (FCAR); Leukocyte immunoglobulin-like receptor subfamily A member 2 (LILRA2); CD300 molecule-like family member f (CD300LF); C-type lectin domain family 12 member A (CLEC12A); bone marrow stromal cell antigen 2 (BST2); EGF-like module-containing mucin-like hormone receptor-like 2 (EMR2); lymphocyte antigen 75 (LY75); Glypican-3 (GPC3); Fc receptor-like 5 (FCRL5); mouse double minute 2 homolog (MDM2); livin; alphafetoprotein (AFP); transmembrane activator and CAML Interactor (TACI); B-cell activating factor receptor (BAFF-R); V-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog (KRAS); immunoglobulin lambda-like polypeptide 1 (IGLL1); 707-AP (707 alanine proline); ART-4 (adenocarcinoma antigen recognized by T4 cells); BAGE (B antigen; b-catenin/m, b-catenin/mutated); CAMEL (CTL-recognized antigen on melanoma); CAP1 (carcinoembryonic antigen peptide 1); CASP-8 (caspase-8); CDC27m (cell-division cycle 27 mutated); CDK4/m (cycline-dependent kinase 4 mutated); Cyp-B (cyclophilin B); DAM (differentiation antigen melanoma); EGP-2 (epithelial glycoprotein 2); EGP-40 (epithelial glycoprotein 40); Erbb2, 3, 4 (erythroblastic leukemia viral oncogene homolog-2, -3, 4); FBP (folate binding protein); fAchR (Fetal acetylcholine receptor); G250 (glycoprotein 250); GAGE (G antigen); GnT-V (N-acetylglucosaminyltransferase V); HAGE (helicose antigen); ULA-A (human leukocyte antigen-A); HST2 (human signet ring tumor 2); KIAA0205; KDR (kinase insert domain receptor); LDLR/FUT (low density lipid receptor/GDP L-fucose: b-D-galactosidase 2-a-L fucosyltransferase); L1CAM (L1 cell adhesion molecule); MC1R (melanocortin 1 receptor); Myosin/m (myosin mutated); MUM-1, -2, -3 (melanoma ubiquitous mutated 1, 2, 3); NA88-A (NA cDNA clone of patient M88); KG2D (Natural killer group 2, member D) ligands; oncofetal antigen (h5T4); p190 minor bcr-abl (protein of 190KD bcr-abl); Pml/RARa (promyelocytic leukaemia/retinoic acid receptor a); PRAME (preferentially expressed antigen of melanoma); SAGE (sarcoma antigen); TEL/AML1 (translocation Ets-family leukemia/acute myeloid leukemia 1); TPI/m (triosephosphate isomerase mutated); and any combination thereof.

In certain embodiments, an antigen to be targeted in adoptive cell therapy (such as particularly CAR or TCR T-cell therapy) of a disease (such as particularly of tumor or cancer) is a tumor-specific antigen (TSA).

In certain embodiments, an antigen to be targeted in adoptive cell therapy (such as particularly CAR or TCR T-cell therapy) of a disease (such as particularly of tumor or cancer) is a neoantigen.

In certain embodiments, an antigen to be targeted in adoptive cell therapy (such as particularly CAR or TCR T-cell therapy) of a disease (such as particularly of tumor or cancer) is a tumor-associated antigen (TAA).

In certain embodiments, an antigen to be targeted in adoptive cell therapy (such as particularly CAR or TCR T-cell therapy) of a disease (such as particularly of tumor or cancer) is a universal tumor antigen. In certain preferred embodiments, the universal tumor antigen is selected from the group consisting of: a human telomerase reverse transcriptase (hTERT), survivin, mouse double minute 2 homolog (MDM2), cytochrome P450 1B 1 (CYP 1B), HER2/neu, Wilms' tumor gene 1 (WT1), livin, alphafetoprotein (AFP), carcinoembryonic antigen (CEA), mucin 16 (MUC16), MUC1, prostate-specific membrane antigen (PSMA), p53, cyclin (D1), and any combinations thereof.

In certain embodiments, an antigen (such as a tumor antigen) to be targeted in adoptive cell therapy (such as particularly CAR or TCR T-cell therapy) of a disease (such as particularly of tumor or cancer) may be selected from a group consisting of: CD19, BCMA, CLL-1, MAGE A3, MAGE A6, HPV E6, HPV E7, WT1, CD22, CD171, ROR1, MUC16, and SSX2. In certain preferred embodiments, the antigen may be CD19. For example, CD19 may be targeted in hematologic malignancies, such as in lymphomas, more particularly in B-cell lymphomas, such as without limitation in diffuse large B-cell lymphoma, primary mediastinal b-cell lymphoma, transformed follicular lymphoma, marginal zone lymphoma, mantle cell lymphoma, acute lymphoblastic leukemia including adult and pediatric ALL, non-Hodgkin lymphoma, indolent non-Hodgkin lymphoma, or chronic lymphocytic leukemia. For example, BCMA may be targeted in multiple myeloma or plasma cell leukemia. For example, CLL1 may be targeted in acute myeloid leukemia. For example, MAGE A3, MAGE A6, SSX2, and/or KRAS may be targeted in solid tumors. For example, HPV E6 and/or HPV E7 may be targeted in cervical cancer or head and neck cancer. For example, WT1 may be targeted in acute myeloid leukemia (AML), myelodysplastic syndromes (MDS), chronic myeloid leukemia (CML), non-small cell lung cancer, breast, pancreatic, ovarian or colorectal cancers, or mesothelioma. For example, CD22 may be targeted in B cell malignancies, including non-Hodgkin lymphoma, diffuse large B-cell lymphoma, or acute lymphoblastic leukemia. For example, CD171 may be targeted in neuroblastoma, glioblastoma, or lung, pancreatic, or ovarian cancers. For example, ROR1 may be targeted in ROR1+ malignancies, including non-small cell lung cancer, triple negative breast cancer, pancreatic cancer, prostate cancer, ALL, chronic lymphocytic leukemia, or mantle cell lymphoma. For example, MUC16 may be targeted in MUC16ecto+ epithelial ovarian, fallopian tube or primary peritoneal cancer.

Various strategies may for example be employed to genetically modify T cells by altering the specificity of the T cell receptor (TCR) for example by introducing new TCR α and β chains with selected peptide specificity (see U.S. Pat. No. 8,697,854; PCT Patent Publications: WO2003020763, WO2004033685, WO2004044004, WO2005114215, WO2006000830, WO2008038002, WO2008039818, WO2004074322, WO2005113595, WO2006125962, WO2013166321, WO2013039889, WO2014018863, WO2014083173; U.S. Pat. No. 8,088,379).

As an alternative to, or addition to, TCR modifications, chimeric antigen receptors (CARs) may be used in order to generate immunoresponsive cells, such as T cells, specific for selected targets, such as malignant cells, with a wide variety of receptor chimera constructs having been described (see U.S. Pat. Nos. 5,843,728; 5,851,828; 5,912,170; 6,004,811; 6,284,240; 6,392,013; 6,410,014; 6,753,162; 8,211,422; and, PCT Publication WO9215322).

In general, CARs are comprised of an extracellular domain, a transmembrane domain, and an intracellular domain, wherein the extracellular domain comprises an antigen-binding domain that is specific for a predetermined target. While the antigen-binding domain of a CAR is often an antibody or antibody fragment (e.g., a single chain variable fragment, scFv), the binding domain is not particularly limited so long as it results in specific recognition of a target. For example, in some embodiments, the antigen-binding domain may comprise a receptor, such that the CAR is capable of binding to the ligand of the receptor. Alternatively, the antigen-binding domain may comprise a ligand, such that the CAR is capable of binding the endogenous receptor of that ligand.

The antigen-binding domain of a CAR is generally separated from the transmembrane domain by a hinge or spacer. The spacer is also not particularly limited, and it is designed to provide the CAR with flexibility. For example, a spacer domain may comprise a portion of a human Fc domain, including a portion of the CH3 domain, or the hinge region of any immunoglobulin, such as IgA, IgD, IgE, IgG, or IgM, or variants thereof. Furthermore, the hinge region may be modified so as to prevent off-target binding by FcRs or other potential interfering objects. For example, the hinge may comprise an IgG4 Fc domain with or without a S228P, L235E, and/or N297Q mutation (according to Kabat numbering) in order to decrease binding to FcRs. Additional spacers/hinges include, but are not limited to, CD4, CD8, and CD28 hinge regions.

The transmembrane domain of a CAR may be derived either from a natural or from a synthetic source. Where the source is natural, the domain may be derived from any membrane bound or transmembrane protein. Transmembrane regions of particular use in this disclosure may be derived from CD8, CD28, CD3, CD45, CD4, CD5, CDS, CD9, CD 16, CD22, CD33, CD37, CD64, CD80, CD86, CD 134, CD137, CD 154, TCR. Alternatively, the transmembrane domain may be synthetic, in which case it will comprise predominantly hydrophobic residues such as leucine and valine. Preferably a triplet of phenylalanine, tryptophan and valine will be found at each end of a synthetic transmembrane domain. Optionally, a short oligo- or polypeptide linker, preferably between 2 and 10 amino acids in length may form the linkage between the transmembrane domain and the cytoplasmic signaling domain of the CAR. A glycine-serine doublet provides a particularly suitable linker.

Alternative CAR constructs may be characterized as belonging to successive generations. First-generation CARs typically consist of a single-chain variable fragment of an antibody specific for an antigen, for example comprising a V_(L) linked to a V_(H) of a specific antibody, linked by a flexible linker, for example by a CD8α hinge domain and a CD8α transmembrane domain, to the transmembrane and intracellular signaling domains of either CD3ζ or FcRγ (scFv-CD3ζ or scFv-FcRγ; see U.S. Pat. Nos. 7,741,465; 5,912,172; 5,906,936). Second-generation CARs incorporate the intracellular domains of one or more costimulatory molecules, such as CD28, OX40 (CD134), or 4-1BB (CD137) within the endodomain (for example scFv-CD28/OX40/4-1BB-CD3ζ; see U.S. Pat. Nos. 8,911,993; 8,916,381; 8,975,071; 9,101,584; 9,102,760; 9,102,761). Third-generation CARs include a combination of costimulatory endodomains, such a CD3ζ-chain, CD97, GDI 1a-CD18, CD2, ICOS, CD27, CD154, CDS, OX40, 4-1BB, CD2, CD7, LIGHT, LFA-1, NKG2C, B7-H3, CD30, CD40, or CD28 signaling domains (for example scFv-CD28-4-1BB-CD3ζ or scFv-CD28-OX40-CD3ζ; see U.S. Pat. Nos. 8,906,682; 8,399,645; 5,686,281; PCT Publication No. WO2014134165; PCT Publication No. WO2012079000). In certain embodiments, the primary signaling domain comprises a functional signaling domain of a protein selected from the group consisting of CD3 zeta, CD3 gamma, CD3 delta, CD3 epsilon, common FcR gamma (FCERIG), FcR beta (Fc Epsilon R1b), CD79a, CD79b, Fc gamma RIIa, DAP10, and DAP12. In certain preferred embodiments, the primary signaling domain comprises a functional signaling domain of CD3ζ or FcRγ. In certain embodiments, the one or more costimulatory signaling domains comprise a functional signaling domain of a protein selected, each independently, from the group consisting of: CD27, CD28, 4-1BB (CD137), OX40, CD30, CD40, ICOS, lymphocyte function-associated antigen-1 (LFA-1), CD2, CD7, LIGHT, NKG2C, B7-H3, a ligand that specifically binds with CD83, CDS, ICAM-1, GITR, BAFFR, HVEM (LIGHTR), SLAMF7, NKp80 (KLRF1), CD160, CD19, CD4, CD8 alpha, CD8 beta, IL2R beta, IL2R gamma, IL7R alpha, ITGA4, VLA1, CD49a, ITGA4, IA4, CD49D, ITGA6, VLA-6, CD49f, ITGAD, CD11d, ITGAE, CD103, ITGAL, CD11a, LFA-1, ITGAM, CD11b, ITGAX, CD11c, ITGB1, CD29, ITGB2, CD18, ITGB7, TNFR2, TRANCE/RANKL, DNAM1 (CD226), SLAMF4 (CD244, 2B4), CD84, CD96 (Tactile), CEACAM1, CRTAM, Ly9 (CD229), CD160 (BY55), PSGL1, CD100 (SEMA4D), CD69, SLAMF6 (NTB-A, Lyl08), SLAM (SLAMF1, CD150, IPO-3), BLAME (SLAMF8), SELPLG (CD162), LTBR, LAT, GADS, SLP-76, PAG/Cbp, NKp44, NKp30, NKp46, and NKG2D. In certain embodiments, the one or more costimulatory signaling domains comprise a functional signaling domain of a protein selected, each independently, from the group consisting of: 4-1BB, CD27, and CD28. In certain embodiments, a chimeric antigen receptor may have the design as described in U.S. Pat. No. 7,446,190, comprising an intracellular domain of CD3ζ chain (such as amino acid residues 52-163 of the human CD3 zeta chain, as shown in SEQ ID NO: 14 of U.S. Pat. No. 7,446,190), a signaling region from CD28 and an antigen-binding element (or portion or domain; such as scFv). The CD28 portion, when between the zeta chain portion and the antigen-binding element, may suitably include the transmembrane and signaling domains of CD28 (such as amino acid residues 114-220 of SEQ ID NO: 10, full sequence shown in SEQ ID NO: 6 of U.S. Pat. No. 7,446,190; these can include the following portion of CD28 as set forth in Genbank identifier NM_006139 (sequence version 1, 2 or 3): IEVMYPPPYLDNEKSNGTIIHVKGKHLCP SPLFPGP SKPFWVLVVVGGVLACYSLLVTVA FIIFWVRSKRSRLLHSDYMNMTPRRPGPTRKHYQPYAPPRDFAAYRS) (SEQ ID NO: 1). Alternatively, when the zeta sequence lies between the CD28 sequence and the antigen-binding element, intracellular domain of CD28 can be used alone (such as amino sequence set forth in SEQ ID NO: 9 of U.S. Pat. No. 7,446,190). Hence, certain embodiments employ a CAR comprising (a) a zeta chain portion comprising the intracellular domain of human CD3ζ chain, (b) a costimulatory signaling region, and (c) an antigen-binding element (or portion or domain), wherein the costimulatory signaling region comprises the amino acid sequence encoded by SEQ ID NO: 6 of U.S. Pat. No. 7,446,190.

Alternatively, costimulation may be orchestrated by expressing CARs in antigen-specific T cells, chosen so as to be activated and expanded following engagement of their native aP3TCR, for example by antigen on professional antigen-presenting cells, with attendant costimulation. In addition, additional engineered receptors may be provided on the immunoresponsive cells, for example to improve targeting of a T-cell attack and/or minimize side effects.

By means of an example and without limitation, Kochenderfer et al., (2009) J Immunother. 32 (7): 689-702 described anti-CD19 chimeric antigen receptors (CAR). FMC63-28Z CAR contained a single chain variable region moiety (scFv) recognizing CD19 derived from the FMC63 mouse hybridoma (described in Nicholson et al., (1997) Molecular Immunology 34: 1157-1165), a portion of the human CD28 molecule, and the intracellular component of the human TCR-molecule. FMC63-CD828BBZ CAR contained the FMC63 scFv, the hinge and transmembrane regions of the CD8 molecule, the cytoplasmic portions of CD28 and 4-1BB, and the cytoplasmic component of the TCR-molecule. The exact sequence of the CD28 molecule included in the FMC63-28Z CAR corresponded to Genbank identifier NM_006139; the sequence included all amino acids starting with the amino acid sequence IEVMYPPPY and continuing all the way to the carboxy-terminus of the protein. To encode the anti-CD19 scFv component of the vector, the authors designed a DNA sequence which was based on a portion of a previously published CAR (Cooper et al., (2003) Blood 101: 1637-1644). This sequence encoded the following components in frame from the 5′ end to the 3′ end: an XhoI site, the human granulocyte-macrophage colony-stimulating factor (GM-CSF) receptor a-chain signal sequence, the FMC63 light chain variable region (as in Nicholson et al., supra), a linker peptide (as in Cooper et al., supra), the FMC63 heavy chain variable region (as in Nicholson et al., supra), and a NotI site. A plasmid encoding this sequence was digested with XhoI and NotI. To form the MSGV-FMC63-28Z retroviral vector, the XhoI and NotI-digested fragment encoding the FMC63 scFv was ligated into a second XhoI and NotI-digested fragment that encoded the MSGV retroviral backbone (as in Hughes et al., (2005) Human Gene Therapy 16: 457-472) as well as part of the extracellular portion of human CD28, the entire transmembrane and cytoplasmic portion of human CD28, and the cytoplasmic portion of the human TCR-molecule (as in Maher et al., 2002) Nature Biotechnology 20: 70-75). The FMC63-28Z CAR is included in the KTE-C19 (axicabtagene ciloleucel) anti-CD19 CAR-T therapy product in development by Kite Pharma, Inc. for the treatment of inter alia patients with relapsed/refractory aggressive B-cell non-Hodgkin lymphoma (NHL). Accordingly, in certain embodiments, cells intended for adoptive cell therapies, more particularly immunoresponsive cells such as T cells, may express the FMC63-28Z CAR as described by Kochenderfer et al. (supra). Hence, in certain embodiments, cells intended for adoptive cell therapies, more particularly immunoresponsive cells such as T cells, may comprise a CAR comprising an extracellular antigen-binding element (or portion or domain; such as scFv) that specifically binds to an antigen, an intracellular signaling domain comprising an intracellular domain of a CD3ζ chain, and a costimulatory signaling region comprising a signaling domain of CD28. Preferably, the CD28 amino acid sequence is as set forth in Genbank identifier NM_006139 (sequence version 1, 2 or 3) starting with the amino acid sequence IEVMYPPPY (SEQ ID NO: 2) and continuing all the way to the carboxy-terminus of the protein. The sequence is reproduced herein: IEVMYPPPYLDNEKSNGTIIHVKGKHLCP SPLFPGP SKPFWVLVVVGGVLACYSLLVTVA FIIFWVRSKRSRLLHSDYMNMTPRRPGPTRKHYQPYAPPRDFAAYRS. Preferably, the antigen is CD19, more preferably the antigen-binding element is an anti-CD19 scFv, even more preferably the anti-CD19 scFv as described by Kochenderfer et al. (supra).

Additional anti-CD19 CARs are further described in WO2015187528. More particularly Example 1 and Table 1 of WO2015187528, incorporated by reference herein, demonstrate the generation of anti-CD19 CARs based on a fully human anti-CD19 monoclonal antibody (47G4, as described in US20100104509) and murine anti-CD 19 monoclonal antibody (as described in Nicholson et al. and explained above). Various combinations of a signal sequence (human CD8-alpha or GM-CSF receptor), extracellular and transmembrane regions (human CD8-alpha) and intracellular T-cell signalling domains (CD28-CD3ζ; 4-1BB-CD3ζ; CD27-CD3ζ; CD28-CD27-CD3ζ, 4-1BB-CD27-CD3ζ; CD27-4-1BB-CD3ζ; CD28-CD27-FcεRI gamma chain; or CD28-FcεRI gamma chain) were disclosed. Hence, in certain embodiments, cells intended for adoptive cell therapies, more particularly immunoresponsive cells such as T cells, may comprise a CAR comprising an extracellular antigen-binding element that specifically binds to an antigen, an extracellular and transmembrane region as set forth in Table 1 of WO2015187528 and an intracellular T-cell signalling domain as set forth in Table 1 of WO2015187528. Preferably, the antigen is CD19, more preferably the antigen-binding element is an anti-CD19 scFv, even more preferably the mouse or human anti-CD19 scFv as described in Example 1 of WO2015187528. In certain embodiments, the CAR comprises, consists essentially of or consists of an amino acid sequence of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, or SEQ ID NO: 13 as set forth in Table 1 ofWO2015187528.

In certain embodiments, the immune cell may, in addition to a CAR or exogenous TCR as described herein, further comprise a chimeric inhibitory receptor (inhibitory CAR) that specifically binds to a second target antigen and is capable of inducing an inhibitory or immunosuppressive or repressive signal to the cell upon recognition of the second target antigen. In certain embodiments, the chimeric inhibitory receptor comprises an extracellular antigen-binding element (or portion or domain) configured to specifically bind to a target antigen, a transmembrane domain, and an intracellular immunosuppressive or repressive signaling domain. In certain embodiments, the second target antigen is an antigen that is not expressed on the surface of a cancer cell or infected cell or the expression of which is downregulated on a cancer cell or an infected cell. In certain embodiments, the second target antigen is an MHC-class I molecule. In certain embodiments, the intracellular signaling domain comprises a functional signaling portion of an immune checkpoint molecule, such as for example PD-1 or CTLA4. Advantageously, the inclusion of such inhibitory CAR reduces the chance of the engineered immune cells attacking non-target (e.g., non-cancer) tissues.

Alternatively, T-cells expressing CARs may be further modified to reduce or eliminate expression of endogenous TCRs in order to reduce off-target effects. Reduction or elimination of endogenous TCRs can reduce off-target effects and increase the effectiveness of the T cells (U.S. Pat. No. 9,181,527). T cells stably lacking expression of a functional TCR may be produced using a variety of approaches. T cells internalize, sort, and degrade the entire T cell receptor as a complex, with a half-life of about 10 hours in resting T cells and 3 hours in stimulated T cells (von Essen, M. et al. 2004. J. Immunol. 173:384-393). Proper functioning of the TCR complex requires the proper stoichiometric ratio of the proteins that compose the TCR complex. TCR function also requires two functioning TCR zeta proteins with ITAM motifs. The activation of the TCR upon engagement of its MHC-peptide ligand requires the engagement of several TCRs on the same T cell, which all must signal properly. Thus, if a TCR complex is destabilized with proteins that do not associate properly or cannot signal optimally, the T cell will not become activated sufficiently to begin a cellular response.

Accordingly, in some embodiments, TCR expression may eliminated using RNA interference (e.g., shRNA, siRNA, miRNA, etc.), CRISPR, or other methods that target the nucleic acids encoding specific TCRs (e.g., TCR-α and TCR-β) and/or CD3 chains in primary T cells. By blocking expression of one or more of these proteins, the T cell will no longer produce one or more of the key components of the TCR complex, thereby destabilizing the TCR complex and preventing cell surface expression of a functional TCR.

In some instances, CAR may also comprise a switch mechanism for controlling expression and/or activation of the CAR. For example, a CAR may comprise an extracellular, transmembrane, and intracellular domain, in which the extracellular domain comprises a target-specific binding element that comprises a label, binding domain, or tag that is specific for a molecule other than the target antigen that is expressed on or by a target cell. In such embodiments, the specificity of the CAR is provided by a second construct that comprises a target antigen binding domain (e.g., an scFv or a bispecific antibody that is specific for both the target antigen and the label or tag on the CAR) and a domain that is recognized by or binds to the label, binding domain, or tag on the CAR. See, e.g., WO 2013/044225, WO 2016/000304, WO 2015/057834, WO 2015/057852, WO 2016/070061, U.S. Pat. No. 9,233,125, US 2016/0129109. In this way, a T-cell that expresses the CAR can be administered to a subject, but the CAR cannot bind its target antigen until the second composition comprising an antigen-specific binding domain is administered.

Alternative switch mechanisms include CARs that require multimerization in order to activate their signaling function (see, e.g., US 2015/0368342, US 2016/0175359, US 2015/0368360) and/or an exogenous signal, such as a small molecule drug (US 2016/0166613, Yung et al., Science, 2015), in order to elicit a T-cell response. Some CARs may also comprise a “suicide switch” to induce cell death of the CAR T-cells following treatment (Buddee et al., PLoS One, 2013) or to downregulate expression of the CAR following binding to the target antigen (WO 2016/011210).

Alternative techniques may be used to transform target immunoresponsive cells, such as protoplast fusion, lipofection, transfection or electroporation. A wide variety of vectors may be used, such as retroviral vectors, lentiviral vectors, adenoviral vectors, adeno-associated viral vectors, plasmids or transposons, such as a Sleeping Beauty transposon (see U.S. Pat. Nos. 6,489,458; 7,148,203; 7,160,682; 7,985,739; 8,227,432), may be used to introduce CARs, for example using 2nd generation antigen-specific CARs signaling through CD3ζ and either CD28 or CD137. Viral vectors may for example include vectors based on HIV, SV40, EBV, HSV or BPV.

Cells that are targeted for transformation may for example include T cells, Natural Killer (NK) cells, cytotoxic T lymphocytes (CTL), regulatory T cells, human embryonic stem cells, tumor-infiltrating lymphocytes (TIL) or a pluripotent stem cell from which lymphoid cells may be differentiated. T cells expressing a desired CAR may for example be selected through co-culture with γ-irradiated activating and propagating cells (AaPC), which co-express the cancer antigen and co-stimulatory molecules. The engineered CAR T-cells may be expanded, for example by co-culture on AaPC in presence of soluble factors, such as IL-2 and IL-21. This expansion may for example be carried out so as to provide memory CAR+ T cells (which may for example be assayed by non-enzymatic digital array and/or multi-panel flow cytometry). In this way, CAR T cells may be provided that have specific cytotoxic activity against antigen-bearing tumors (optionally in conjunction with production of desired chemokines such as interferon-γ). CAR T cells of this kind may for example be used in animal models, for example to treat tumor xenografts.

Unlike T-cell receptors (TCRs) that are MHC restricted, CARs can potentially bind any cell surface-expressed antigen and can thus be more universally used to treat patients (see Irving et al., Engineering Chimeric Antigen Receptor T-Cells for Racing in Solid Tumors: Don't Forget the Fuel, Front. Immunol., 3 Apr. 2017, doi.org/10.3389/fimmu.2017.00267). In certain embodiments, in the absence of endogenous T-cell infiltrate (e.g., due to aberrant antigen processing and presentation), which precludes the use of TIL therapy and immune checkpoint blockade, the transfer of CAR T-cells may be used to treat patients (see, e.g., Hinrichs C S, Rosenberg S A. Exploiting the curative potential of adoptive T-cell therapy for cancer. Immunol Rev (2014) 257(1):56-71. doi:10.1111/imr.12132).

Approaches such as the foregoing may be adapted to provide methods of treating and/or increasing survival of a subject having a disease, such as a neoplasia, for example by administering an effective amount of an immunoresponsive cell comprising an antigen recognizing receptor that binds a selected antigen, wherein the binding activates the immunoresponsive cell, thereby treating or preventing the disease (such as a neoplasia, a pathogen infection, an autoimmune disorder, or an allogeneic transplant reaction).

In certain embodiments, the treatment can be administered after lymphodepleting pretreatment in the form of chemotherapy (typically a combination of cyclophosphamide and fludarabine) or radiation therapy. Initial studies in ACT had short lived responses and the transferred cells did not persist in vivo for very long (Houot et al., T-cell-based immunotherapy: adoptive cell transfer and checkpoint inhibition. Cancer Immunol Res (2015) 3(10): 1115-22; and Kamta et al., Advancing Cancer Therapy with Present and Emerging Immuno-Oncology Approaches. Front. Oncol. (2017) 7:64). Immune suppressor cells like Tregs and MDSCs may attenuate the activity of transferred cells by outcompeting them for the necessary cytokines. Not being bound by a theory lymphodepleting pretreatment may eliminate the suppressor cells allowing the TILs to persist. In certain embodiments, transferred cells can be depleted for the suppressive T cells of the present invention. Not being bound by a theory, only effector cells are transferred and the transferred cells may persist longer.

In one embodiment, the treatment can be administrated into patients undergoing an immunosuppressive treatment. The cells or population of cells, may be made resistant to at least one immunosuppressive agent due to the inactivation of a gene encoding a receptor for such immunosuppressive agent. Not being bound by a theory, the immunosuppressive treatment should help the selection and expansion of the immunoresponsive or T cells according to the invention within the patient.

In certain embodiments, the treatment can be administered before primary treatment (e.g., surgery or radiation therapy) to shrink a tumor before the primary treatment. In another embodiment, the treatment can be administered after primary treatment to remove any remaining cancer cells.

In certain embodiments, immunometabolic barriers can be targeted therapeutically prior to and/or during ACT to enhance responses to ACT or CAR T-cell therapy and to support endogenous immunity (see, e.g., Irving et al., Engineering Chimeric Antigen Receptor T-Cells for Racing in Solid Tumors: Don't Forget the Fuel, Front. Immunol., 3 Apr. 2017, doi.org/10.33 89/fimmu.2017.00267).

The administration of cells or population of cells, such as immune system cells or cell populations, such as more particularly immunoresponsive cells or cell populations, as disclosed herein may be carried out in any convenient manner, including by aerosol inhalation, injection, ingestion, transfusion, implantation or transplantation. The cells or population of cells may be administered to a patient subcutaneously, intradermally, intratumorally, intranodally, intramedullary, intramuscularly, intrathecally, by intravenous or intralymphatic injection, or intraperitoneally. In some embodiments, the disclosed CARs may be delivered or administered into a cavity formed by the resection of tumor tissue (i.e. intracavity delivery) or directly into a tumor prior to resection (i.e. intratumoral delivery). In one embodiment, the cell compositions of the present invention are preferably administered by intravenous injection.

The administration of the cells or population of cells can consist of the administration of 10⁴-10⁹ cells per kg body weight, preferably 10⁵ to 10⁶ cells/kg body weight including all integer values of cell numbers within those ranges. Dosing in CAR T cell therapies may for example involve administration of from 10⁶ to 10⁹ cells/kg, with or without a course of lymphodepletion, for example with cyclophosphamide. The cells or population of cells can be administrated in one or more doses. In another embodiment, the effective amount of cells are administrated as a single dose. In another embodiment, the effective amount of cells are administrated as more than one dose over a period time. Timing of administration is within the judgment of managing physician and depends on the clinical condition of the patient. The cells or population of cells may be obtained from any source, such as a blood bank or a donor. While individual needs vary, determination of optimal ranges of effective amounts of a given cell type for a particular disease or conditions are within the skill of one in the art. An effective amount means an amount which provides a therapeutic or prophylactic benefit. The dosage administrated will be dependent upon the age, health and weight of the recipient, kind of concurrent treatment, if any, frequency of treatment and the nature of the effect desired.

In another embodiment, the effective amount of cells or composition comprising those cells are administrated parenterally. The administration can be an intravenous administration. The administration can be directly done by injection within a tumor.

To guard against possible adverse reactions, engineered immunoresponsive cells may be equipped with a transgenic safety switch, in the form of a transgene that renders the cells vulnerable to exposure to a specific signal. For example, the herpes simplex viral thymidine kinase (TK) gene may be used in this way, for example by introduction into allogeneic T lymphocytes used as donor lymphocyte infusions following stem cell transplantation (Greco, et al., Improving the safety of cell therapy with the TK-suicide gene. Front. Pharmacol. 2015; 6: 95). In such cells, administration of a nucleoside prodrug such as ganciclovir or acyclovir causes cell death. Alternative safety switch constructs include inducible caspase 9, for example triggered by administration of a small-molecule dimerizer that brings together two nonfunctional icasp9 molecules to form the active enzyme. A wide variety of alternative approaches to implementing cellular proliferation controls have been described (see U.S. Patent Publication No. 20130071414; PCT Patent Publication WO2011146862; PCT Patent Publication WO2014011987; PCT Patent Publication WO2013040371; Zhou et al. BLOOD, 2014, 123/25:3895-3905; Di Stasi et al., The New England Journal of Medicine 2011; 365:1673-1683; Sadelain M, The New England Journal of Medicine 2011; 365:1735-173; Ramos et al., Stem Cells 28(6):1107-15 (2010)).

In a further refinement of adoptive therapies, genome editing may be used to tailor immunoresponsive cells to alternative implementations, for example providing edited CAR T cells (see Poirot et al., 2015, Multiplex genome edited T-cell manufacturing platform for “off-the-shelf” adoptive T-cell immunotherapies, Cancer Res 75 (18): 3853; Ren et al., 2016, Multiplex genome editing to generate universal CAR T cells resistant to PD1 inhibition, Clin Cancer Res. 2016 Nov. 4; and Qasim et al., 2017, Molecular remission of infant B-ALL after infusion of universal TALEN gene-edited CAR T cells, Sci Transl Med. 2017 Jan. 25; 9(374)). Cells may be edited using any CRISPR system and method of use thereof as described herein. CRISPR systems may be delivered to an immune cell by any method described herein. In preferred embodiments, cells are edited ex vivo and transferred to a subject in need thereof. Immunoresponsive cells, CAR T cells or any cells used for adoptive cell transfer may be edited. Editing may be performed for example to insert or knock-in an exogenous gene, such as an exogenous gene encoding a CAR or a TCR, at a preselected locus in a cell; to eliminate potential alloreactive T-cell receptors (TCR) or to prevent inappropriate pairing between endogenous and exogenous TCR chains, such as to knock-out or knock-down expression of an endogenous TCR in a cell; to disrupt the target of a chemotherapeutic agent in a cell; to block an immune checkpoint, such as to knock-out or knock-down expression of an immune checkpoint protein or receptor in a cell; to knock-out or knock-down expression of other gene or genes in a cell, the reduced expression or lack of expression of which can enhance the efficacy of adoptive therapies using the cell; to knock-out or knock-down expression of an endogenous gene in a cell, said endogenous gene encoding an antigen targeted by an exogenous CAR or TCR; to knock-out or knock-down expression of one or more MHC constituent proteins in a cell; to activate a T cell; to modulate cells such that the cells are resistant to exhaustion or dysfunction; and/or increase the differentiation and/or proliferation of functionally exhausted or dysfunctional CD8+ T-cells (see PCT Patent Publications: WO2013176915, WO2014059173, WO2014172606, WO2014184744, and WO2014191128). Editing may result in inactivation of a gene.

By inactivating a gene it is intended that the gene of interest is not expressed in a functional protein form. In a particular embodiment, the CRISPR system specifically catalyzes cleavage in one targeted gene thereby inactivating said targeted gene. The nucleic acid strand breaks caused are commonly repaired through the distinct mechanisms of homologous recombination or non-homologous end joining (NHEJ). However, NHEJ is an imperfect repair process that often results in changes to the DNA sequence at the site of the cleavage. Repair via non-homologous end joining (NHEJ) often results in small insertions or deletions (Indel) and can be used for the creation of specific gene knockouts. Cells in which a cleavage induced mutagenesis event has occurred can be identified and/or selected by well-known methods in the art.

Hence, in certain embodiments, editing of cells (such as by CRISPR/Cas), particularly cells intended for adoptive cell therapies, more particularly immunoresponsive cells such as T cells, may be performed to insert or knock-in an exogenous gene, such as an exogenous gene encoding a CAR or a TCR, at a preselected locus in a cell. Conventionally, nucleic acid molecules encoding CARs or TCRs are transfected or transduced to cells using randomly integrating vectors, which, depending on the site of integration, may lead to clonal expansion, oncogenic transformation, variegated transgene expression and/or transcriptional silencing of the transgene. Directing of transgene(s) to a specific locus in a cell can minimize or avoid such risks and advantageously provide for uniform expression of the transgene(s) by the cells. Without limitation, suitable ‘safe harbor’ loci for directed transgene integration include CCR5 or AAVS 1. Homology-directed repair (HDR) strategies are known and described elsewhere in this specification allowing to insert transgenes into desired loci.

Further suitable loci for insertion of transgenes, in particular CAR or exogenous TCR transgenes, include without limitation loci comprising genes coding for constituents of endogenous T-cell receptor, such as T-cell receptor alpha locus (TRA) or T-cell receptor beta locus (TRB), for example T-cell receptor alpha constant (TRAC) locus, T-cell receptor beta constant 1 (TRBC1) locus or T-cell receptor beta constant 2 (TRBC1) locus. Advantageously, insertion of a transgene into such locus can simultaneously achieve expression of the transgene, potentially controlled by the endogenous promoter, and knock-out expression of the endogenous TCR. This approach has been exemplified in Eyquem et al., (2017) Nature 543: 113-117, wherein the authors used CRISPR/Cas9 gene editing to knock-in a DNA molecule encoding a CD19-specific CAR into the TRAC locus downstream of the endogenous promoter; the CAR-T cells obtained by CRISPR were significantly superior in terms of reduced tonic CAR signaling and exhaustion.

T cell receptors (TCR) are cell surface receptors that participate in the activation of T cells in response to the presentation of antigen. The TCR is generally made from two chains, a and β, which assemble to form a heterodimer and associates with the CD3-transducing subunits to form the T cell receptor complex present on the cell surface. Each α and β chain of the TCR consists of an immunoglobulin-like N-terminal variable (V) and constant (C) region, a hydrophobic transmembrane domain, and a short cytoplasmic region. As for immunoglobulin molecules, the variable region of the a and 3 chains are generated by V(D)J recombination, creating a large diversity of antigen specificities within the population of T cells. However, in contrast to immunoglobulins that recognize intact antigen, T cells are activated by processed peptide fragments in association with an MHC molecule, introducing an extra dimension to antigen recognition by T cells, known as MHC restriction. Recognition of MHC disparities between the donor and recipient through the T cell receptor leads to T cell proliferation and the potential development of graft versus host disease (GVHD). The inactivation of TCRa or TCRP3 can result in the elimination of the TCR from the surface of T cells preventing recognition of alloantigen and thus GVHD. However, TCR disruption generally results in the elimination of the CD3 signaling component and alters the means of further T cell expansion.

Hence, in certain embodiments, editing of cells (such as by CRISPR/Cas), particularly cells intended for adoptive cell therapies, more particularly immunoresponsive cells such as T cells, may be performed to knock-out or knock-down expression of an endogenous TCR in a cell. For example, NHEJ-based or HDR-based gene editing approaches can be employed to disrupt the endogenous TCR alpha and/or beta chain genes. For example, gene editing system or systems, such as CRISPR/Cas system or systems, can be designed to target a sequence found within the TCR beta chain conserved between the beta 1 and beta 2 constant region genes (TRBC1 and TRBC2) and/or to target the constant region of the TCR alpha chain (TRAC) gene.

Allogeneic cells are rapidly rejected by the host immune system. It has been demonstrated that, allogeneic leukocytes present in non-irradiated blood products will persist for no more than 5 to 6 days (Boni, Muranski et al. 2008 Blood 1; 112(12):4746-54). Thus, to prevent rejection of allogeneic cells, the host's immune system usually has to be suppressed to some extent. However, in the case of adoptive cell transfer the use of immunosuppressive drugs also have a detrimental effect on the introduced therapeutic T cells. Therefore, to effectively use an adoptive immunotherapy approach in these conditions, the introduced cells would need to be resistant to the immunosuppressive treatment. Thus, in a particular embodiment, the present invention further comprises a step of modifying T cells to make them resistant to an immunosuppressive agent, preferably by inactivating at least one gene encoding a target for an immunosuppressive agent. An immunosuppressive agent is an agent that suppresses immune function by one of several mechanisms of action. An immunosuppressive agent can be, but is not limited to a calcineurin inhibitor, a target of rapamycin, an interleukin-2 receptor a-chain blocker, an inhibitor of inosine monophosphate dehydrogenase, an inhibitor of dihydrofolic acid reductase, a corticosteroid or an immunosuppressive antimetabolite. The present invention allows conferring immunosuppressive resistance to T cells for immunotherapy by inactivating the target of the immunosuppressive agent in T cells. As non-limiting examples, targets for an immunosuppressive agent can be a receptor for an immunosuppressive agent such as: CD52, glucocorticoid receptor (GR), a FKBP family gene member and a cyclophilin family gene member.

In certain embodiments, editing of cells (such as by CRISPR/Cas), particularly cells intended for adoptive cell therapies, more particularly immunoresponsive cells such as T cells, may be performed to block an immune checkpoint, such as to knock-out or knock-down expression of an immune checkpoint protein or receptor in a cell. Immune checkpoints are inhibitory pathways that slow down or stop immune reactions and prevent excessive tissue damage from uncontrolled activity of immune cells. In certain embodiments, the immune checkpoint targeted is the programmed death-1 (PD-1 or CD279) gene (PDCD1). In other embodiments, the immune checkpoint targeted is cytotoxic T-lymphocyte-associated antigen (CTLA-4). In additional embodiments, the immune checkpoint targeted is another member of the CD28 and CTLA4 Ig superfamily such as TIM-3, BTLA, LAG3, ICOS, PDL1 or KIR.

Additional immune checkpoints include Src homology 2 domain-containing protein tyrosine phosphatase 1 (SHP-1) (Watson H A, et al., SHP-1: the next checkpoint target for cancer immunotherapy? Biochem Soc Trans. 2016 Apr. 15; 44(2):356-62). SHP-1 is a widely expressed inhibitory protein tyrosine phosphatase (PTP). In T-cells, it is a negative regulator of antigen-dependent activation and proliferation. It is a cytosolic protein, and therefore not amenable to antibody-mediated therapies, but its role in activation and proliferation makes it an attractive target for genetic manipulation in adoptive transfer strategies, such as chimeric antigen receptor (CAR) T cells. Immune checkpoints may also include T cell immunoreceptor with Ig and ITIM domains (TIGIT/Vstm3/WUCAMIVSIG9) and VISTA (Le Mercier I, et al., (2015) Beyond CTLA-4 and PD-1, the generation Z of negative checkpoint regulators. Front. Immunol. 6:418).

WO2014172606 relates to the use of MT1 and/or MT2 inhibitors to increase proliferation and/or activity of exhausted CD8+ T-cells and to decrease CD8+ T-cell exhaustion (e.g., decrease functionally exhausted or unresponsive CD8+ immune cells). In certain embodiments, metallothioneins are targeted by gene editing in adoptively transferred T cells.

In certain embodiments, editing of cells (such as by CRISPR/Cas), particularly cells intended for adoptive cell therapies, more particularly immunoresponsive cells such as T cells, may be performed to enhance or maintain expression of co-stimulatory receptors (co-stimulatory immune checkpoint molecule), such as a member of the TNFR superfamily including, but not limited to CD40, OX40, CD137 (4-1BB), GITR or CD27.

In certain embodiments, targets of gene editing may be at least one targeted locus involved in the expression of an immune checkpoint protein. Such targets may include, but are not limited to CTLA4, PPP2CA, PPP2CB, PTPN6, PTPN22, PDCD1, ICOS (CD278), PDL1, KIR, LAG3, HAVCR2, BTLA, CD160, TIGIT, CD96, CRTAM, LAIR1, SIGLEC7, SIGLEC9, CD244 (2B4), TNFRSF10B, TNFRSF10A, CASP8, CASP10, CASP3, CASP6, CASP7, FADD, FAS, TGFBRII, TGFRBRI, SMAD2, SMAD3, SMAD4, SMAD10, SKI, SKIL, TGIF1, IL10RA, IL10RB, HMOX2, IL6R, IL6ST, EIF2AK4, CSK, PAG1, SIT1, FOXP3, PRDM1, BATF, VISTA, GUCY1A2, GUCY1A3, GUCY1B2, GUCY1B3, MT1, MT2, CD40, OX40, CD137, GITR, CD27, SHP-1, TIM-3, CEACAM-1, CEACAM-3, or CEACAM-5. In preferred embodiments, the gene locus involved in the expression of PD-1 or CTLA-4 genes is targeted. In other preferred embodiments, combinations of genes are targeted, such as but not limited to PD-1 and TIGIT.

By means of an example and without limitation, WO2016196388 concerns an engineered T cell comprising (a) a genetically engineered antigen receptor that specifically binds to an antigen, which receptor may be a CAR; and (b) a disrupted gene encoding a PD-L1, an agent for disruption of a gene encoding a PD-L1, and/or disruption of a gene encoding PD-L1, wherein the disruption of the gene may be mediated by a gene editing nuclease, a zinc finger nuclease (ZFN), CRISPR/Cas9 and/or TALEN. WO2015142675 relates to immune effector cells comprising a CAR in combination with an agent (such as CRISPR, TALEN or ZFN) that increases the efficacy of the immune effector cells in the treatment of cancer, wherein the agent may inhibit an immune inhibitory molecule, such as PD1, PD-L1, CTLA-4, TIM-3, LAG-3, VISTA, BTLA, TIGIT, LAIR1, CD160, 2B4, TGFR beta, CEACAM-1, CEACAM-3, or CEACAM-5. Ren et al., (2017) Clin Cancer Res 23 (9) 2255-2266 performed lentiviral delivery of CAR and electro-transfer of Cas9 mRNA and gRNAs targeting endogenous TCR, 0-2 microglobulin (B2M) and PD1 simultaneously, to generate gene-disrupted allogeneic CAR T cells deficient of TCR, HLA class I molecule and PD1.

In certain embodiments, cells may be engineered to express a CAR, wherein expression and/or function of methylcytosine dioxygenase genes (TET1, TET2 and/or TET3) in the cells has been reduced or eliminated, such as by CRISPR, ZNF or TALEN (for example, as described in WO201704916).

In certain embodiments, editing of cells (such as by CRISPR/Cas), particularly cells intended for adoptive cell therapies, more particularly immunoresponsive cells such as T cells, may be performed to knock-out or knock-down expression of an endogenous gene in a cell, said endogenous gene encoding an antigen targeted by an exogenous CAR or TCR, thereby reducing the likelihood of targeting of the engineered cells. In certain embodiments, the targeted antigen may be one or more antigen selected from the group consisting of CD38, CD138, CS-1, CD33, CD26, CD30, CD53, CD92, CD100, CD148, CD150, CD200, CD261, CD262, CD362, human telomerase reverse transcriptase (hTERT), survivin, mouse double minute 2 homolog (MDM2), cytochrome P450 1B1 (CYP1B), HER2/neu, Wilms' tumor gene 1 (WT1), livin, alphafetoprotein (AFP), carcinoembryonic antigen (CEA), mucin 16 (MUC16), MUC1, prostate-specific membrane antigen (PSMA), p53, cyclin (D1), B cell maturation antigen (BCMA), transmembrane activator and CAML Interactor (TACI), and B-cell activating factor receptor (BAFF-R) (for example, as described in WO2016011210 and WO2017011804).

In certain embodiments, editing of cells (such as by CRISPR/Cas), particularly cells intended for adoptive cell therapies, more particularly immunoresponsive cells such as T cells, may be performed to knock-out or knock-down expression of one or more MHC constituent proteins, such as one or more HLA proteins and/or beta-2 microglobulin (B2M), in a cell, whereby rejection of non-autologous (e.g., allogeneic) cells by the recipient's immune system can be reduced or avoided. In preferred embodiments, one or more HLA class I proteins, such as HLA-A, B and/or C, and/or B2M may be knocked-out or knocked-down. Preferably, B2M may be knocked-out or knocked-down. By means of an example, Ren et al., (2017) Clin Cancer Res 23 (9) 2255-2266 performed lentiviral delivery of CAR and electro-transfer of Cas9 mRNA and gRNAs targeting endogenous TCR, β-2 microglobulin (B2M) and PD1 simultaneously, to generate gene-disrupted allogeneic CAR T cells deficient of TCR, HLA class I molecule and PD1.

In other embodiments, at least two genes are edited. Pairs of genes may include, but are not limited to PD1 and TCRα, PD1 and TCRβ, CTLA-4 and TCRα, CTLA-4 and TCRβ, LAG3 and TCRα, LAG3 and TCRβ, Tim3 and TCRα, Tim3 and TCRβ, BTLA and TCRα, BTLA and TCRβ, BY55 and TCRα, BY55 and TCRβ, TIGIT and TCRα, TIGIT and TCRβ, B7H5 and TCRα, B7H5 and TCRβ, LAIR1 and TCRα, LAIR1 and TCRβ, SIGLEC10 and TCRα, SIGLEC10 and TCRP3, 2B4 and TCRα, 2B4 and TCRβ.

In certain embodiments, a cell may be multiply edited (multiplex genome editing) as taught herein to (1) knock-out or knock-down expression of an endogenous TCR (for example, TRBC1, TRBC2 and/or TRAC), (2) knock-out or knock-down expression of an immune checkpoint protein or receptor (for example PD1, PD-L1 and/or CTLA4); and (3) knock-out or knock-down expression of one or more MHC constituent proteins (for example, HLA-A, B and/or C, and/or B2M, preferably B2M).

Whether prior to or after genetic modification of the T cells, the T cells can be activated and expanded generally using methods as described, for example, in U.S. Pat. Nos. 6,352,694; 6,534,055; 6,905,680; 5,858,358; 6,887,466; 6,905,681; 7,144,575; 7,232,566; 7,175,843; 5,883,223; 6,905,874; 6,797,514; 6,867,041; and 7,572,631. T cells can be expanded in vitro or in vivo.

Immune cells may be obtained using any method known in the art. In one embodiment T cells that have infiltrated a tumor are isolated. T cells may be removed during surgery. T cells may be isolated after removal of tumor tissue by biopsy. T cells may be isolated by any means known in the art. In one embodiment, the method may comprise obtaining a bulk population of T cells from a tumor sample by any suitable method known in the art. For example, a bulk population of T cells can be obtained from a tumor sample by dissociating the tumor sample into a cell suspension from which specific cell populations can be selected. Suitable methods of obtaining a bulk population of T cells may include, but are not limited to, any one or more of mechanically dissociating (e.g., mincing) the tumor, enzymatically dissociating (e.g., digesting) the tumor, and aspiration (e.g., as with a needle).

The bulk population of T cells obtained from a tumor sample may comprise any suitable type of T cell. Preferably, the bulk population of T cells obtained from a tumor sample comprises tumor infiltrating lymphocytes (TILs).

The tumor sample may be obtained from any mammal. Unless stated otherwise, as used herein, the term “mammal” refers to any mammal including, but not limited to, mammals of the order Logomorpha, such as rabbits; the order Carnivora, including Felines (cats) and Canines (dogs); the order Artiodactyla, including Bovines (cows) and Swines (pigs); or of the order Perssodactyla, including Equines (horses). The mammals may be non-human primates, e.g., of the order Primates, Ceboids, or Simoids (monkeys) or of the order Anthropoids (humans and apes). In some embodiments, the mammal may be a mammal of the order Rodentia, such as mice and hamsters. Preferably, the mammal is a non-human primate or a human. An especially preferred mammal is the human.

T cells can be obtained from a number of sources, including peripheral blood mononuclear cells, bone marrow, lymph node tissue, spleen tissue, and tumors. In certain embodiments of the present invention, T cells can be obtained from a unit of blood collected from a subject using any number of techniques known to the skilled artisan, such as Ficoll separation. In one preferred embodiment, cells from the circulating blood of an individual are obtained by apheresis or leukapheresis. The apheresis product typically contains lymphocytes, including T cells, monocytes, granulocytes, B cells, other nucleated white blood cells, red blood cells, and platelets. In one embodiment, the cells collected by apheresis may be washed to remove the plasma fraction and to place the cells in an appropriate buffer or media for subsequent processing steps. In one embodiment of the invention, the cells are washed with phosphate buffered saline (PBS). In an alternative embodiment, the wash solution lacks calcium and may lack magnesium or may lack many if not all divalent cations. Initial activation steps in the absence of calcium lead to magnified activation. As those of ordinary skill in the art would readily appreciate a washing step may be accomplished by methods known to those in the art, such as by using a semi-automated “flow-through” centrifuge (for example, the Cobe 2991 cell processor) according to the manufacturer's instructions. After washing, the cells may be resuspended in a variety of biocompatible buffers, such as, for example, Ca-free, Mg-free PBS. Alternatively, the undesirable components of the apheresis sample may be removed and the cells directly resuspended in culture media.

In another embodiment, T cells are isolated from peripheral blood lymphocytes by lysing the red blood cells and depleting the monocytes, for example, by centrifugation through a PERCOLL™ gradient.

A specific subpopulation of T cells can be further isolated by positive or negative selection techniques. For example, in one preferred embodiment, T cells are isolated by incubation with antibody-conjugated beads (e.g., specific for any marker described herein), such as DYNABEADS® for a time period sufficient for positive selection of the desired T cells. In one embodiment, the time period is about 30 minutes. In a further embodiment, the time period ranges from 30 minutes to 36 hours or longer and all integer values there between. In a further embodiment, the time period is at least 1, 2, 3, 4, 5, or 6 hours. In yet another preferred embodiment, the time period is 10 to 24 hours. In one preferred embodiment, the incubation time period is 24 hours. For isolation of T cells from patients with leukemia, use of longer incubation times, such as 24 hours, can increase cell yield. Longer incubation times may be used to isolate T cells in any situation where there are few T cells as compared to other cell types, such in isolating tumor infiltrating lymphocytes (TIL) from tumor tissue or from immunocompromised individuals. Further, use of longer incubation times can increase the efficiency of capture of CD8+ T cells.

Enrichment of a T cell population by negative selection can be accomplished with a combination of antibodies directed to surface markers unique to the negatively selected cells. A preferred method is cell sorting and/or selection via negative magnetic immunoadherence or flow cytometry that uses a cocktail of monoclonal antibodies directed to cell surface markers present on the cells negatively selected.

Further, monocyte populations (i.e., CD14+ cells) may be depleted from blood preparations by a variety of methodologies, including anti-CD14 coated beads or columns, or utilization of the phagocytotic activity of these cells to facilitate removal. Accordingly, in one embodiment, the invention uses paramagnetic particles of a size sufficient to be engulfed by phagocytotic monocytes. In certain embodiments, the paramagnetic particles are commercially available beads, for example, those produced by Life Technologies under the trade name Dynabeads™. In one embodiment, other non-specific cells are removed by coating the paramagnetic particles with “irrelevant” proteins (e.g., serum proteins or antibodies). Irrelevant proteins and antibodies include those proteins and antibodies or fragments thereof that do not specifically target the T cells to be isolated. In certain embodiments the irrelevant beads include beads coated with sheep anti-mouse antibodies, goat anti-mouse antibodies, and human serum albumin.

In brief, such depletion of monocytes is performed by preincubating T cells isolated from whole blood, apheresed peripheral blood, or tumors with one or more varieties of irrelevant or non-antibody coupled paramagnetic particles at any amount that allows for removal of monocytes (approximately a 20:1 bead:cell ratio) for about 30 minutes to 2 hours at 22 to 37 degrees C., followed by magnetic removal of cells which have attached to or engulfed the paramagnetic particles. Such separation can be performed using standard methods available in the art. For example, any magnetic separation methodology may be used including a variety of which are commercially available, (e.g., DYNAL® Magnetic Particle Concentrator (DYNAL MPC®)). Assurance of requisite depletion can be monitored by a variety of methodologies known to those of ordinary skill in the art, including flow cytometric analysis of CD14 positive cells, before and after depletion.

For isolation of a desired population of cells by positive or negative selection, the concentration of cells and surface (e.g., particles such as beads) can be varied. In certain embodiments, it may be desirable to significantly decrease the volume in which beads and cells are mixed together (i.e., increase the concentration of cells), to ensure maximum contact of cells and beads. For example, in one embodiment, a concentration of 2 billion cells/ml is used. In one embodiment, a concentration of 1 billion cells/ml is used. In a further embodiment, greater than 100 million cells/ml is used. In a further embodiment, a concentration of cells of 10, 15, 20, 25, 30, 35, 40, 45, or 50 million cells/ml is used. In yet another embodiment, a concentration of cells from 75, 80, 85, 90, 95, or 100 million cells/ml is used. In further embodiments, concentrations of 125 or 150 million cells/ml can be used. Using high concentrations can result in increased cell yield, cell activation, and cell expansion. Further, use of high cell concentrations allows more efficient capture of cells that may weakly express target antigens of interest or from samples where there are many tumor cells present (i.e., leukemic blood, tumor tissue, etc). Such populations of cells may have therapeutic value and would be desirable to obtain.

In a related embodiment, it may be desirable to use lower concentrations of cells. By significantly diluting the mixture of T cells and surface (e.g., particles such as beads), interactions between the particles and cells is minimized. This selects for cells that express high amounts of desired antigens to be bound to the particles. In one embodiment, the concentration of cells used is 5×10⁶/ml. In other embodiments, the concentration used can be from about 1×10⁵/ml to 1×10⁶/ml, and any integer value in between.

In certain embodiments, T cells can also be frozen. Wishing not to be bound by theory, the freeze and subsequent thaw step provides a more uniform product by removing granulocytes and to some extent monocytes in the cell population. After a washing step to remove plasma and platelets, the cells may be suspended in a freezing solution. While many freezing solutions and parameters are known in the art and will be useful in this context, one method involves using PBS containing 20% DMSO and 8% human serum albumin, or other suitable cell freezing media, the cells then are frozen to −80° C. at a rate of 1° per minute and stored in the vapor phase of a liquid nitrogen storage tank. Other methods of controlled freezing may be used as well as uncontrolled freezing immediately at −20° C. or in liquid nitrogen.

T cells for use in the present invention may also be antigen-specific T cells. For example, tumor-specific T cells can be used. In certain embodiments, antigen-specific T cells can be isolated from a patient of interest, such as a patient afflicted with a cancer or an infectious disease. In one embodiment neoepitopes are determined for a subject and T cells specific to these antigens are isolated. Antigen-specific cells for use in expansion may also be generated in vitro using any number of methods known in the art, for example, as described in U.S. Patent Publication No. US 20040224402 entitled, Generation and Isolation of Antigen-Specific T Cells, or in U.S. Pat. No. 6,040,177. Antigen-specific cells for use in the present invention may also be generated using any number of methods known in the art, for example, as described in Current Protocols in Immunology, or Current Protocols in Cell Biology, both published by John Wiley & Sons, Inc., Boston, Mass.

In a related embodiment, it may be desirable to sort or otherwise positively select (e.g. via magnetic selection) the antigen specific cells prior to or following one or two rounds of expansion. Sorting or positively selecting antigen-specific cells can be carried out using peptide-MHC tetramers (Altman, et al., Science. 1996 Oct. 4; 274(5284):94-6). In another embodiment the adaptable tetramer technology approach is used (Andersen et al., 2012 Nat Protoc. 7:891-902). Tetramers are limited by the need to utilize predicted binding peptides based on prior hypotheses, and the restriction to specific HLAs. Peptide-MHC tetramers can be generated using techniques known in the art and can be made with any MHC molecule of interest and any antigen of interest as described herein. Specific epitopes to be used in this context can be identified using numerous assays known in the art. For example, the ability of a polypeptide to bind to MHC class I may be evaluated indirectly by monitoring the ability to promote incorporation of ¹²⁵I labeled J32-microglobulin (132m) into MHC class I/02m/peptide heterotrimeric complexes (see Parker et al., J. Immunol. 152:163, 1994).

In one embodiment cells are directly labeled with an epitope-specific reagent for isolation by flow cytometry followed by characterization of phenotype and TCRs. In one T cells are isolated by contacting the T cell specific antibodies. Sorting of antigen-specific T cells, or generally any cells of the present invention, can be carried out using any of a variety of commercially available cell sorters, including, but not limited to, MoFlo sorter (DakoCytomation, Fort Collins, Colo.), FACSAria™, FACSArray™, FACSVantage™, BD™ LSR II, and FACSCalibur™ (BD Biosciences, San Jose, Calif.).

In a preferred embodiment, the method comprises selecting cells that also express CD3. The method may comprise specifically selecting the cells in any suitable manner. Preferably, the selecting is carried out using flow cytometry. The flow cytometry may be carried out using any suitable method known in the art. The flow cytometry may employ any suitable antibodies and stains. Preferably, the antibody is chosen such that it specifically recognizes and binds to the particular biomarker being selected. For example, the specific selection of CD3, CD8, TIM-3, LAG-3, 4-1BB, or PD-1 may be carried out using anti-CD3, anti-CD8, anti-TIM-3, anti-LAG-3, anti-4-1BB, or anti-PD-1 antibodies, respectively. The antibody or antibodies may be conjugated to a bead (e.g., a magnetic bead) or to a fluorochrome. Preferably, the flow cytometry is fluorescence-activated cell sorting (FACS). TCRs expressed on T cells can be selected based on reactivity to autologous tumors. Additionally, T cells that are reactive to tumors can be selected for based on markers using the methods described in patent publication Nos. WO2014133567 and WO2014133568, herein incorporated by reference in their entirety. Additionally, activated T cells can be selected for based on surface expression of CD107a.

In one embodiment of the invention, the method further comprises expanding the numbers of T cells in the enriched cell population. Such methods are described in U.S. Pat. No. 8,637,307 and is herein incorporated by reference in its entirety. The numbers of T cells may be increased at least about 3-fold (or 4-, 5-, 6-, 7-, 8-, or 9-fold), more preferably at least about 10-fold (or 20-, 30-, 40-, 50-, 60-, 70-, 80-, or 90-fold), more preferably at least about 100-fold, more preferably at least about 1,000 fold, or most preferably at least about 100,000-fold. The numbers of T cells may be expanded using any suitable method known in the art. Exemplary methods of expanding the numbers of cells are described in patent publication No. WO 2003057171, U.S. Pat. No. 8,034,334, and U.S. Patent Application Publication No. 2012/0244133, each of which is incorporated herein by reference.

In one embodiment, ex vivo T cell expansion can be performed by isolation of T cells and subsequent stimulation or activation followed by further expansion. In one embodiment of the invention, the T cells may be stimulated or activated by a single agent. In another embodiment, T cells are stimulated or activated with two agents, one that induces a primary signal and a second that is a co-stimulatory signal. Ligands useful for stimulating a single signal or stimulating a primary signal and an accessory molecule that stimulates a second signal may be used in soluble form. Ligands may be attached to the surface of a cell, to an Engineered Multivalent Signaling Platform (EMSP), or immobilized on a surface. In a preferred embodiment both primary and secondary agents are co-immobilized on a surface, for example a bead or a cell. In one embodiment, the molecule providing the primary activation signal may be a CD3 ligand, and the co-stimulatory molecule may be a CD28 ligand or 4-1BB ligand.

In certain embodiments, T cells comprising a CAR or an exogenous TCR, may be manufactured as described in WO2015120096, by a method comprising: enriching a population of lymphocytes obtained from a donor subject; stimulating the population of lymphocytes with one or more T-cell stimulating agents to produce a population of activated T cells, wherein the stimulation is performed in a closed system using serum-free culture medium; transducing the population of activated T cells with a viral vector comprising a nucleic acid molecule which encodes the CAR or TCR, using a single cycle transduction to produce a population of transduced T cells, wherein the transduction is performed in a closed system using serum-free culture medium; and expanding the population of transduced T cells for a predetermined time to produce a population of engineered T cells, wherein the expansion is performed in a closed system using serum-free culture medium. In certain embodiments, T cells comprising a CAR or an exogenous TCR, may be manufactured as described in WO2015120096, by a method comprising: obtaining a population of lymphocytes; stimulating the population of lymphocytes with one or more stimulating agents to produce a population of activated T cells, wherein the stimulation is performed in a closed system using serum-free culture medium; transducing the population of activated T cells with a viral vector comprising a nucleic acid molecule which encodes the CAR or TCR, using at least one cycle transduction to produce a population of transduced T cells, wherein the transduction is performed in a closed system using serum-free culture medium; and expanding the population of transduced T cells to produce a population of engineered T cells, wherein the expansion is performed in a closed system using serum-free culture medium. The predetermined time for expanding the population of transduced T cells may be 3 days. The time from enriching the population of lymphocytes to producing the engineered T cells may be 6 days. The closed system may be a closed bag system. Further provided is population of T cells comprising a CAR or an exogenous TCR obtainable or obtained by said method, and a pharmaceutical composition comprising such cells.

In certain embodiments, T cell maturation or differentiation in vitro may be delayed or inhibited by the method as described in WO2017070395, comprising contacting one or more T cells from a subject in need of a T cell therapy with an AKT inhibitor (such as, e.g., one or a combination of two or more AKT inhibitors disclosed in claim 8 of WO2017070395) and at least one of exogenous Interleukin-7 (IL-7) and exogenous Interleukin-15 (IL-15), wherein the resulting T cells exhibit delayed maturation or differentiation, and/or wherein the resulting T cells exhibit improved T cell function (such as, e.g., increased T cell proliferation; increased cytokine production; and/or increased cytolytic activity) relative to a T cell function of a T cell cultured in the absence of an AKT inhibitor.

In certain embodiments, a patient in need of a T cell therapy may be conditioned by a method as described in WO2016191756 comprising administering to the patient a dose of cyclophosphamide between 200 mg/m²/day and 2000 mg/m²/day and a dose of fludarabine between 20 mg/m²/day and 900 mg/m²/day.

In one embodiment, adoptive cell transfer may comprise: depleting T cells as defined herein from a population of T cells obtained from the subject; in vitro expanding the T cell population; and administering the in vitro expanded T cell population to the subject. In certain embodiments, the method may further comprise formulating the in vitro expanded immune cell or immune cell population into a pharmaceutical composition.

In certain embodiments, suppressive CD8+ T cells are administered in combination with an autoimmune drug. Non-limiting examples of such drugs include methotrexate, cyclophosphamide, Imuran (azathioprine), cyclosporin, and steroid compounds such as prednisone and methylprednisolone.

Genetic Modifying Agents

In certain embodiments, the one or more modulating agents may be a genetic modifying agent or an epigenetic modifying agent. The genetic modifying agent may comprise a CRISPR system, a zinc finger nuclease system, a TALEN, or a meganuclease. The epigenetic modifying agent may comprise a DNA methylation inhibitor, HDAC inhibitor, histone acetylation inhibitor, histone methylation inhibitor or histone demethylase inhibitor.

In general, a CRISPR-Cas or CRISPR system as used in herein and in documents, such as WO 2014/093622 (PCT/US2013/074667), refers collectively to transcripts and other elements involved in the expression of or directing the activity of CRISPR-associated (“Cas”) genes, including sequences encoding a Cas gene, a tracr (trans-activating CRISPR) sequence (e.g. tracrRNA or an active partial tracrRNA), a tracr-mate sequence (encompassing a “direct repeat” and a tracrRNA-processed partial direct repeat in the context of an endogenous CRISPR system), a guide sequence (also referred to as a “spacer” in the context of an endogenous CRISPR system), or “RNA(s)” as that term is herein used (e.g., RNA(s) to guide Cas, such as Cas9, e.g. CRISPR RNA and transactivating (tracr) RNA or a single guide RNA (sgRNA) (chimeric RNA)) or other sequences and transcripts from a CRISPR locus. In general, a CRISPR system is characterized by elements that promote the formation of a CRISPR complex at the site of a target sequence (also referred to as a protospacer in the context of an endogenous CRISPR system). See, e.g, Shmakov et al. (2015) “Discovery and Functional Characterization of Diverse Class 2 CRISPR-Cas Systems”, Molecular Cell, DOI: dx.doi.org/10.1016/j.molcel.2015.10.008.

In certain embodiments, a protospacer adjacent motif (PAM) or PAM-like motif directs binding of the effector protein complex as disclosed herein to the target locus of interest. In some embodiments, the PAM may be a 5′ PAM (i.e., located upstream of the 5′ end of the protospacer). In other embodiments, the PAM may be a 3′ PAM (i.e., located downstream of the 5′ end of the protospacer). The term “PAM” may be used interchangeably with the term “PFS” or “protospacer flanking site” or “protospacer flanking sequence”.

In a preferred embodiment, the CRISPR effector protein may recognize a 3′ PAM. In certain embodiments, the CRISPR effector protein may recognize a 3′ PAM which is 5′H, wherein His A, CorU.

In the context of formation of a CRISPR complex, “target sequence” refers to a sequence to which a guide sequence is designed to have complementarity, where hybridization between a target sequence and a guide sequence promotes the formation of a CRISPR complex. A target sequence may comprise RNA polynucleotides. The term “target RNA” refers to a RNA polynucleotide being or comprising the target sequence. In other words, the target RNA may be a RNA polynucleotide or a part of a RNA polynucleotide to which a part of the gRNA, i.e. the guide sequence, is designed to have complementarity and to which the effector function mediated by the complex comprising CRISPR effector protein and a gRNA is to be directed. In some embodiments, a target sequence is located in the nucleus or cytoplasm of a cell.

In certain example embodiments, the CRISPR effector protein may be delivered using a nucleic acid molecule encoding the CRISPR effector protein. The nucleic acid molecule encoding a CRISPR effector protein, may advantageously be a codon optimized CRISPR effector protein. An example of a codon optimized sequence, is in this instance a sequence optimized for expression in eukaryote, e.g., humans (i.e. being optimized for expression in humans), or for another eukaryote, animal or mammal as herein discussed; see, e.g., SaCas9 human codon optimized sequence in WO 2014/093622 (PCT/US2013/074667). Whilst this is preferred, it will be appreciated that other examples are possible and codon optimization for a host species other than human, or for codon optimization for specific organs is known. In some embodiments, an enzyme coding sequence encoding a CRISPR effector protein is a codon optimized for expression in particular cells, such as eukaryotic cells. The eukaryotic cells may be those of or derived from a particular organism, such as a plant or a mammal, including but not limited to human, or non-human eukaryote or animal or mammal as herein discussed, e.g., mouse, rat, rabbit, dog, livestock, or non-human mammal or primate. In some embodiments, processes for modifying the germ line genetic identity of human beings and/or processes for modifying the genetic identity of animals which are likely to cause them suffering without any substantial medical benefit to man or animal, and also animals resulting from such processes, may be excluded. In general, codon optimization refers to a process of modifying a nucleic acid sequence for enhanced expression in the host cells of interest by replacing at least one codon (e.g. about or more than about 1, 2, 3, 4, 5, 10, 15, 20, 25, 50, or more codons) of the native sequence with codons that are more frequently or most frequently used in the genes of that host cell while maintaining the native amino acid sequence. Various species exhibit particular bias for certain codons of a particular amino acid. Codon bias (differences in codon usage between organisms) often correlates with the efficiency of translation of messenger RNA (mRNA), which is in turn believed to be dependent on, among other things, the properties of the codons being translated and the availability of particular transfer RNA (tRNA) molecules. The predominance of selected tRNAs in a cell is generally a reflection of the codons used most frequently in peptide synthesis. Accordingly, genes can be tailored for optimal gene expression in a given organism based on codon optimization. Codon usage tables are readily available, for example, at the “Codon Usage Database” available at kazusa.orjp/codon/and these tables can be adapted in a number of ways. See Nakamura, Y., et al. “Codon usage tabulated from the international DNA sequence databases: status for the year 2000” Nucl. Acids Res. 28:292 (2000). Computer algorithms for codon optimizing a particular sequence for expression in a particular host cell are also available, such as Gene Forge (Aptagen; Jacobus, Pa.), are also available. In some embodiments, one or more codons (e.g. 1, 2, 3, 4, 5, 10, 15, 20, 25, 50, or more, or all codons) in a sequence encoding a Cas correspond to the most frequently used codon for a particular amino acid.

In certain embodiments, the methods as described herein may comprise providing a Cas transgenic cell in which one or more nucleic acids encoding one or more guide RNAs are provided or introduced operably connected in the cell with a regulatory element comprising a promoter of one or more gene of interest. As used herein, the term “Cas transgenic cell” refers to a cell, such as a eukaryotic cell, in which a Cas gene has been genomically integrated. The nature, type, or origin of the cell are not particularly limiting according to the present invention. Also the way the Cas transgene is introduced in the cell may vary and can be any method as is known in the art. In certain embodiments, the Cas transgenic cell is obtained by introducing the Cas transgene in an isolated cell. In certain other embodiments, the Cas transgenic cell is obtained by isolating cells from a Cas transgenic organism. By means of example, and without limitation, the Cas transgenic cell as referred to herein may be derived from a Cas transgenic eukaryote, such as a Cas knock-in eukaryote. Reference is made to WO 2014/093622 (PCT/US13/74667), incorporated herein by reference. Methods of US Patent Publication Nos. 20120017290 and 20110265198 assigned to Sangamo BioSciences, Inc. directed to targeting the Rosa locus may be modified to utilize the CRISPR Cas system of the present invention. Methods of US Patent Publication No. 20130236946 assigned to Cellectis directed to targeting the Rosa locus may also be modified to utilize the CRISPR Cas system of the present invention. By means of further example reference is made to Platt et. al. (Cell; 159(2):440-455 (2014)), describing a Cas9 knock-in mouse, which is incorporated herein by reference. The Cas transgene can further comprise a Lox-Stop-polyA-Lox(LSL) cassette thereby rendering Cas expression inducible by Cre recombinase. Alternatively, the Cas transgenic cell may be obtained by introducing the Cas transgene in an isolated cell. Delivery systems for transgenes are well known in the art. By means of example, the Cas transgene may be delivered in for instance eukaryotic cell by means of vector (e.g., AAV, adenovirus, lentivirus) and/or particle and/or nanoparticle delivery, as also described herein elsewhere.

It will be understood by the skilled person that the cell, such as the Cas transgenic cell, as referred to herein may comprise further genomic alterations besides having an integrated Cas gene or the mutations arising from the sequence specific action of Cas when complexed with RNA capable of guiding Cas to a target locus.

In certain aspects the invention involves vectors, e.g. for delivering or introducing in a cell Cas and/or RNA capable of guiding Cas to a target locus (i.e. guide RNA), but also for propagating these components (e.g. in prokaryotic cells). A used herein, a “vector” is a tool that allows or facilitates the transfer of an entity from one environment to another. It is a replicon, such as a plasmid, phage, or cosmid, into which another DNA segment may be inserted so as to bring about the replication of the inserted segment. Generally, a vector is capable of replication when associated with the proper control elements. In general, the term “vector” refers to a nucleic acid molecule capable of transporting another nucleic acid to which it has been linked. Vectors include, but are not limited to, nucleic acid molecules that are single-stranded, double-stranded, or partially double-stranded; nucleic acid molecules that comprise one or more free ends, no free ends (e.g. circular); nucleic acid molecules that comprise DNA, RNA, or both; and other varieties of polynucleotides known in the art. One type of vector is a “plasmid,” which refers to a circular double stranded DNA loop into which additional DNA segments can be inserted, such as by standard molecular cloning techniques. Another type of vector is a viral vector, wherein virally-derived DNA or RNA sequences are present in the vector for packaging into a virus (e.g. retroviruses, replication defective retroviruses, adenoviruses, replication defective adenoviruses, and adeno-associated viruses (AAVs)). Viral vectors also include polynucleotides carried by a virus for transfection into a host cell. Certain vectors are capable of autonomous replication in a host cell into which they are introduced (e.g. bacterial vectors having a bacterial origin of replication and episomal mammalian vectors). Other vectors (e.g., non-episomal mammalian vectors) are integrated into the genome of a host cell upon introduction into the host cell, and thereby are replicated along with the host genome. Moreover, certain vectors are capable of directing the expression of genes to which they are operatively-linked. Such vectors are referred to herein as “expression vectors.” Common expression vectors of utility in recombinant DNA techniques are often in the form of plasmids.

Recombinant expression vectors can comprise a nucleic acid of the invention in a form suitable for expression of the nucleic acid in a host cell, which means that the recombinant expression vectors include one or more regulatory elements, which may be selected on the basis of the host cells to be used for expression, that is operatively-linked to the nucleic acid sequence to be expressed. Within a recombinant expression vector, “operably linked” is intended to mean that the nucleotide sequence of interest is linked to the regulatory element(s) in a manner that allows for expression of the nucleotide sequence (e.g. in an in vitro transcription/translation system or in a host cell when the vector is introduced into the host cell). With regards to recombination and cloning methods, mention is made of U.S. patent application Ser. No. 10/815,730, published Sep. 2, 2004 as US 2004-0171156 A1, the contents of which are herein incorporated by reference in their entirety. Thus, the embodiments disclosed herein may also comprise transgenic cells comprising the CRISPR effector system. In certain example embodiments, the transgenic cell may function as an individual discrete volume. In other words samples comprising a masking construct may be delivered to a cell, for example in a suitable delivery vesicle and if the target is present in the delivery vesicle the CRISPR effector is activated and a detectable signal generated.

The vector(s) can include the regulatory element(s), e.g., promoter(s). The vector(s) can comprise Cas encoding sequences, and/or a single, but possibly also can comprise at least 3 or 8 or 16 or 32 or 48 or 50 guide RNA(s) (e.g., sgRNAs) encoding sequences, such as 1-2, 1-3, 1-4 1-5, 3-6, 3-7, 3-8, 3-9, 3-10, 3-8, 3-16, 3-30, 3-32, 3-48, 3-50 RNA(s) (e.g., sgRNAs). In a single vector there can be a promoter for each RNA (e.g., sgRNA), advantageously when there are up to about 16 RNA(s); and, when a single vector provides for more than 16 RNA(s), one or more promoter(s) can drive expression of more than one of the RNA(s), e.g., when there are 32 RNA(s), each promoter can drive expression of two RNA(s), and when there are 48 RNA(s), each promoter can drive expression of three RNA(s). By simple arithmetic and well established cloning protocols and the teachings in this disclosure one skilled in the art can readily practice the invention as to the RNA(s) for a suitable exemplary vector such as AAV, and a suitable promoter such as the U6 promoter. For example, the packaging limit of AAV is ˜4.7 kb. The length of a single U6-gRNA (plus restriction sites for cloning) is 361 bp. Therefore, the skilled person can readily fit about 12-16, e.g., 13 U6-gRNA cassettes in a single vector. This can be assembled by any suitable means, such as a golden gate strategy used for TALE assembly (genome-engineering.org/taleffectors/). The skilled person can also use a tandem guide strategy to increase the number of U6-gRNAs by approximately 1.5 times, e.g., to increase from 12-16, e.g., 13 to approximately 18-24, e.g., about 19 U6-gRNAs. Therefore, one skilled in the art can readily reach approximately 18-24, e.g., about 19 promoter-RNAs, e.g., U6-gRNAs in a single vector, e.g., an AAV vector. A further means for increasing the number of promoters and RNAs in a vector is to use a single promoter (e.g., U6) to express an array of RNAs separated by cleavable sequences. And an even further means for increasing the number of promoter-RNAs in a vector, is to express an array of promoter-RNAs separated by cleavable sequences in the intron of a coding sequence or gene; and, in this instance it is advantageous to use a polymerase II promoter, which can have increased expression and enable the transcription of long RNA in a tissue specific manner. (see, e.g., nar.oxfordjournals.org/content/34/7/e53. short and nature.com/mt/journal/v16/n9/abs/mt2008144a.html). In an advantageous embodiment, AAV may package U6 tandem gRNA targeting up to about 50 genes. Accordingly, from the knowledge in the art and the teachings in this disclosure the skilled person can readily make and use vector(s), e.g., a single vector, expressing multiple RNAs or guides under the control or operatively or functionally linked to one or more promoters—especially as to the numbers of RNAs or guides discussed herein, without any undue experimentation.

The guide RNA(s) encoding sequences and/or Cas encoding sequences, can be functionally or operatively linked to regulatory element(s) and hence the regulatory element(s) drive expression. The promoter(s) can be constitutive promoter(s) and/or conditional promoter(s) and/or inducible promoter(s) and/or tissue specific promoter(s). The promoter can be selected from the group consisting of RNA polymerases, pol I, pol II, pol III, T7, U6, H1, retroviral Rous sarcoma virus (RSV) LTR promoter, the cytomegalovirus (CMV) promoter, the SV40 promoter, the dihydrofolate reductase promoter, the β-actin promoter, the phosphoglycerol kinase (PGK) promoter, and the EF1α promoter. An advantageous promoter is the promoter is U6.

Additional effectors for use according to the invention can be identified by their proximity to casl genes, for example, though not limited to, within the region 20 kb from the start of the casl gene and 20 kb from the end of the casl gene. In certain embodiments, the effector protein comprises at least one HEPN domain and at least 500 amino acids, and wherein the C2c2 effector protein is naturally present in a prokaryotic genome within 20 kb upstream or downstream of a Cas gene or a CRISPR array. Non-limiting examples of Cas proteins include Cas1, Cas1B, Cas2, Cas3, Cas4, Cas5, Cas6, Cas7, Cas8, Cas9 (also known as Csn1 and Csx12), Cas10, Csy1, Csy2, Csy3, Cse1, Cse2, Csc1, Csc2, Csa5, Csn2, Csm2, Csm3, Csm4, Csm5, Csm6, Cmr1, Cmr3, Cmr4, Cmr5, Cmr6, Csb1, Csb2, Csb3, Csx17, Csx14, Csx10, Csx16, CsaX, Csx3, Csx1, Csx15, Csf1, Csf2, Csf3, Csf4, homologues thereof, or modified versions thereof. In certain example embodiments, the C2c2 effector protein is naturally present in a prokaryotic genome within 20kb upstream or downstream of a Cas 1 gene. The terms “orthologue” (also referred to as “ortholog” herein) and “homologue” (also referred to as “homolog” herein) are well known in the art. By means of further guidance, a “homologue” of a protein as used herein is a protein of the same species which performs the same or a similar function as the protein it is a homologue of. Homologous proteins may but need not be structurally related, or are only partially structurally related. An “orthologue” of a protein as used herein is a protein of a different species which performs the same or a similar function as the protein it is an orthologue of. Orthologous proteins may but need not be structurally related, or are only partially structurally related.

Guide Molecules

The methods described herein may be used to screen inhibition of CRISPR systems employing different types of guide molecules. As used herein, the term “guide sequence” and “guide molecule” in the context of a CRISPR-Cas system, comprises any polynucleotide sequence having sufficient complementarity with a target nucleic acid sequence to hybridize with the target nucleic acid sequence and direct sequence-specific binding of a nucleic acid-targeting complex to the target nucleic acid sequence. The guide sequences made using the methods disclosed herein may be a full-length guide sequence, a truncated guide sequence, a full-length sgRNA sequence, a truncated sgRNA sequence, or an E+F sgRNA sequence. In some embodiments, the degree of complementarity of the guide sequence to a given target sequence, when optimally aligned using a suitable alignment algorithm, is about or more than about 50%, 60%, 75%, 80%, 85%, 90%, 95%, 97.5%, 99%, or more. In certain example embodiments, the guide molecule comprises a guide sequence that may be designed to have at least one mismatch with the target sequence, such that a RNA duplex formed between the guide sequence and the target sequence. Accordingly, the degree of complementarity is preferably less than 99%. For instance, where the guide sequence consists of 24 nucleotides, the degree of complementarity is more particularly about 96% or less. In particular embodiments, the guide sequence is designed to have a stretch of two or more adjacent mismatching nucleotides, such that the degree of complementarity over the entire guide sequence is further reduced. For instance, where the guide sequence consists of 24 nucleotides, the degree of complementarity is more particularly about 96% or less, more particularly, about 92% or less, more particularly about 88% or less, more particularly about 84% or less, more particularly about 80% or less, more particularly about 76% or less, more particularly about 72% or less, depending on whether the stretch of two or more mismatching nucleotides encompasses 2, 3, 4, 5, 6 or 7 nucleotides, etc. In some embodiments, aside from the stretch of one or more mismatching nucleotides, the degree of complementarity, when optimally aligned using a suitable alignment algorithm, is about or more than about 50%, 60%, 75%, 80%, 85%, 90%, 95%, 97.5%, 99%, or more. Optimal alignment may be determined with the use of any suitable algorithm for aligning sequences, non-limiting example of which include the Smith-Waterman algorithm, the Needleman-Wunsch algorithm, algorithms based on the Burrows-Wheeler Transform (e.g., the Burrows Wheeler Aligner), ClustalW, Clustal X, BLAT, Novoalign (Novocraft Technologies; available at www.novocraft.com), ELAND (Illumina, San Diego, Calif.), SOAP (available at soap.genomics.org.cn), and Maq (available at maq.sourceforge.net). The ability of a guide sequence (within a nucleic acid-targeting guide RNA) to direct sequence-specific binding of a nucleic acid-targeting complex to a target nucleic acid sequence may be assessed by any suitable assay. For example, the components of a nucleic acid-targeting CRISPR system sufficient to form a nucleic acid-targeting complex, including the guide sequence to be tested, may be provided to a host cell having the corresponding target nucleic acid sequence, such as by transfection with vectors encoding the components of the nucleic acid-targeting complex, followed by an assessment of preferential targeting (e.g., cleavage) within the target nucleic acid sequence, such as by Surveyor assay as described herein. Similarly, cleavage of a target nucleic acid sequence (or a sequence in the vicinity thereof) may be evaluated in a test tube by providing the target nucleic acid sequence, components of a nucleic acid-targeting complex, including the guide sequence to be tested and a control guide sequence different from the test guide sequence, and comparing binding or rate of cleavage at or in the vicinity of the target sequence between the test and control guide sequence reactions. Other assays are possible, and will occur to those skilled in the art. A guide sequence, and hence a nucleic acid-targeting guide RNA may be selected to target any target nucleic acid sequence.

In certain embodiments, the guide sequence or spacer length of the guide molecules is from 15 to 50 nt. In certain embodiments, the spacer length of the guide RNA is at least 15 nucleotides. In certain embodiments, the spacer length is from 15 to 17 nt, e.g., 15, 16, or 17 nt, from 17 to 20 nt, e.g., 17, 18, 19, or 20 nt, from 20 to 24 nt, e.g., 20, 21, 22, 23, or 24 nt, from 23 to 25 nt, e.g., 23, 24, or 25 nt, from 24 to 27 nt, e.g., 24, 25, 26, or 27 nt, from 27-30 nt, e.g., 27, 28, 29, or 30 nt, from 30-35 nt, e.g., 30, 31, 32, 33, 34, or 35 nt, or 35 nt or longer. In certain example embodiment, the guide sequence is 15, 16, 17,18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39 40, 41, 42, 43, 44, 45, 46, 47 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100 nt.

In some embodiments, the guide sequence is an RNA sequence of between 10 to 50 nt in length, but more particularly of about 20-30 nt advantageously about 20 nt, 23-25 nt or 24 nt. The guide sequence is selected so as to ensure that it hybridizes to the target sequence. This is described more in detail below. Selection can encompass further steps which increase efficacy and specificity.

In some embodiments, the guide sequence has a canonical length (e.g., about 15-30 nt) is used to hybridize with the target RNA or DNA. In some embodiments, a guide molecule is longer than the canonical length (e.g., >30 nt) is used to hybridize with the target RNA or DNA, such that a region of the guide sequence hybridizes with a region of the RNA or DNA strand outside of the Cas-guide target complex. This can be of interest where additional modifications, such deamination of nucleotides is of interest. In alternative embodiments, it is of interest to maintain the limitation of the canonical guide sequence length.

In some embodiments, the sequence of the guide molecule (direct repeat and/or spacer) is selected to reduce the degree secondary structure within the guide molecule. In some embodiments, about or less than about 75%, 50%, 40%, 30%, 25%, 20%, 15%, 10%, 5%, 1%, or fewer of the nucleotides of the nucleic acid-targeting guide RNA participate in self-complementary base pairing when optimally folded. Optimal folding may be determined by any suitable polynucleotide folding algorithm. Some programs are based on calculating the minimal Gibbs free energy. An example of one such algorithm is mFold, as described by Zuker and Stiegler (Nucleic Acids Res. 9 (1981), 133-148). Another example folding algorithm is the online webserver RNAfold, developed at Institute for Theoretical Chemistry at the University of Vienna, using the centroid structure prediction algorithm (see e.g., A. R. Gruber et al., 2008, Cell 106(1): 23-24; and PA Carr and GM Church, 2009, Nature Biotechnology 27(12): 1151-62).

In some embodiments, it is of interest to reduce the susceptibility of the guide molecule to RNA cleavage, such as to cleavage by Cas13. Accordingly, in particular embodiments, the guide molecule is adjusted to avoide cleavage by Cas13 or other RNA-cleaving enzymes.

In certain embodiments, the guide molecule comprises non-naturally occurring nucleic acids and/or non-naturally occurring nucleotides and/or nucleotide analogs, and/or chemically modifications. Preferably, these non-naturally occurring nucleic acids and non-naturally occurring nucleotides are located outside the guide sequence. Non-naturally occurring nucleic acids can include, for example, mixtures of naturally and non-naturally occurring nucleotides. Non-naturally occurring nucleotides and/or nucleotide analogs may be modified at the ribose, phosphate, and/or base moiety. In an embodiment of the invention, a guide nucleic acid comprises ribonucleotides and non-ribonucleotides. In one such embodiment, a guide comprises one or more ribonucleotides and one or more deoxyribonucleotides. In an embodiment of the invention, the guide comprises one or more non-naturally occurring nucleotide or nucleotide analog such as a nucleotide with phosphorothioate linkage, a locked nucleic acid (LNA) nucleotides comprising a methylene bridge between the 2′ and 4′ carbons of the ribose ring, or bridged nucleic acids (BNA). Other examples of modified nucleotides include 2′-O-methyl analogs, 2′-deoxy analogs, or 2′-fluoro analogs. Further examples of modified bases include, but are not limited to, 2-aminopurine, 5-bromo-uridine, pseudouridine, inosine, 7-methylguanosine. Examples of guide RNA chemical modifications include, without limitation, incorporation of 2′-O-methyl (M), 2′-O-methyl 3′ phosphorothioate (MS), S-constrained ethyl(cEt), or 2′-O-methyl 3′ thioPACE (MSP) at one or more terminal nucleotides. Such chemically modified guides can comprise increased stability and increased activity as compared to unmodified guides, though on-target vs. off-target specificity is not predictable. (See, Hendel, 2015, Nat Biotechnol. 33(9):985-9, doi: 10.1038/nbt.3290, published online 29 Jun. 2015 Ragdarm et al., 0215, PNAS, E7110-E7111; Allerson et al., J. Med. Chem. 2005, 48:901-904; Bramsen et al., Front. Genet., 2012, 3:154; Deng et al., PNAS, 2015, 112:11870-11875; Sharma et al., MedChemComm., 2014, 5:1454-1471; Hendel et al., Nat. Biotechnol. (2015) 33(9): 985-989; Li et al., Nature Biomedical Engineering, 2017, 1, 0066 DOI:10.1038/s41551-017-0066). In some embodiments, the 5′ and/or 3′ end of a guide RNA is modified by a variety of functional moieties including fluorescent dyes, polyethylene glycol, cholesterol, proteins, or detection tags. (See Kelly et al., 2016, J. Biotech. 233:74-83). In certain embodiments, a guide comprises ribonucleotides in a region that binds to a target RNA and one or more deoxyribonucletides and/or nucleotide analogs in a region that binds to Cas13. In an embodiment of the invention, deoxyribonucleotides and/or nucleotide analogs are incorporated in engineered guide structures, such as, without limitation, stem-loop regions, and the seed region. For Cas13 guide, in certain embodiments, the modification is not in the 5′-handle of the stem-loop regions. Chemical modification in the 5′-handle of the stem-loop region of a guide may abolish its function (see Li, et al., Nature Biomedical Engineering, 2017, 1:0066). In certain embodiments, at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 40, 45, 50, or 75 nucleotides of a guide is chemically modified. In some embodiments, 3-5 nucleotides at either the 3′ or the 5′ end of a guide is chemically modified. In some embodiments, only minor modifications are introduced in the seed region, such as 2′-F modifications. In some embodiments, 2′-F modification is introduced at the 3′ end of a guide. In certain embodiments, three to five nucleotides at the 5′ and/or the 3′ end of the guide are chemicially modified with 2′-O-methyl (M), 2′-O-methyl 3′ phosphorothioate (MS), S-constrained ethyl(cEt), or 2′-O-methyl 3′ thioPACE (MSP). Such modification can enhance genome editing efficiency (see Hendel et al., Nat. Biotechnol. (2015) 33(9): 985-989). In certain embodiments, all of the phosphodiester bonds of a guide are substituted with phosphorothioates (PS) for enhancing levels of gene disruption. In certain embodiments, more than five nucleotides at the 5′ and/or the 3′ end of the guide are chemicially modified with 2′-O-Me, 2′-F or S-constrained ethyl(cEt). Such chemically modified guide can mediate enhanced levels of gene disruption (see Ragdarm et al., 0215, PNAS, E7110-E7111). In an embodiment of the invention, a guide is modified to comprise a chemical moiety at its 3′ and/or 5′ end. Such moieties include, but are not limited to amine, azide, alkyne, thio, dibenzocyclooctyne (DBCO), or Rhodamine. In certain embodiment, the chemical moiety is conjugated to the guide by a linker, such as an alkyl chain. In certain embodiments, the chemical moiety of the modified guide can be used to attach the guide to another molecule, such as DNA, RNA, protein, or nanoparticles. Such chemically modified guide can be used to identify or enrich cells generically edited by a CRISPR system (see Lee et al., eLife, 2017, 6:e25312, DOI:10.7554).

In some embodiments, the modification to the guide is a chemical modification, an insertion, a deletion or a split. In some embodiments, the chemical modification includes, but is not limited to, incorporation of 2′-O-methyl (M) analogs, 2′-deoxy analogs, 2-thiouridine analogs, N6-methyladenosine analogs, 2′-fluoro analogs, 2-aminopurine, 5-bromo-uridine, pseudouridine (Ψ), N1-methylpseudouridine (melΨ), 5-methoxyuridine(5moU), inosine, 7-methylguanosine, 2′-O-methyl 3′phosphorothioate (MS), S-constrained ethyl(cEt), phosphorothioate (PS), or 2′-O-methyl 3′thioPACE (MSP). In some embodiments, the guide comprises one or more of phosphorothioate modifications. In certain embodiments, at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or 25 nucleotides of the guide are chemically modified. In certain embodiments, one or more nucleotides in the seed region are chemically modified. In certain embodiments, one or more nucleotides in the 3′-terminus are chemically modified. In certain embodiments, none of the nucleotides in the 5′-handle is chemically modified. In some embodiments, the chemical modification in the seed region is a minor modification, such as incorporation of a 2′-fluoro analog. In a specific embodiment, one nucleotide of the seed region is replaced with a 2′-fluoro analog. In some embodiments, 5 to 10 nucleotides in the 3′-terminus are chemically modified. Such chemical modifications at the 3′-terminus of the Cas13 CrRNA may improve Cas13 activity. In a specific embodiment, 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 nucleotides in the 3′-terminus are replaced with 2′-fluoro analogues. In a specific embodiment, 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 nucleotides in the 3′-terminus are replaced with 2′-O-methyl (M) analogs.

In some embodiments, the loop of the 5′-handle of the guide is modified. In some embodiments, the loop of the 5′-handle of the guide is modified to have a deletion, an insertion, a split, or chemical modifications. In certain embodiments, the modified loop comprises 3, 4, or 5 nucleotides. In certain embodiments, the loop comprises the sequence of UCUU, UUUU, UAUU, or UGUU (SEQ ID NOs: 3-6).

In some embodiments, the guide molecule forms a stemloop with a separate non-covalently linked sequence, which can be DNA or RNA. In particular embodiments, the sequences forming the guide are first synthesized using the standard phosphoramidite synthetic protocol (Herdewijn, P., ed., Methods in Molecular Biology Col 288, Oligonucleotide Synthesis: Methods and Applications, Humana Press, New Jersey (2012)). In some embodiments, these sequences can be functionalized to contain an appropriate functional group for ligation using the standard protocol known in the art (Hermanson, G. T., Bioconjugate Techniques, Academic Press (2013)). Examples of functional groups include, but are not limited to, hydroxyl, amine, carboxylic acid, carboxylic acid halide, carboxylic acid active ester, aldehyde, carbonyl, chlorocarbonyl, imidazolylcarbonyl, hydrozide, semicarbazide, thio semicarbazide, thiol, maleimide, haloalkyl, sufonyl, ally, propargyl, diene, alkyne, and azide. Once this sequence is functionalized, a covalent chemical bond or linkage can be formed between this sequence and the direct repeat sequence. Examples of chemical bonds include, but are not limited to, those based on carbamates, ethers, esters, amides, imines, amidines, aminotrizines, hydrozone, disulfides, thioethers, thioesters, phosphorothioates, phosphorodithioates, sulfonamides, sulfonates, fulfones, sulfoxides, ureas, thioureas, hydrazide, oxime, triazole, photolabile linkages, C—C bond forming groups such as Diels-Alder cyclo-addition pairs or ring-closing metathesis pairs, and Michael reaction pairs.

In some embodiments, these stem-loop forming sequences can be chemically synthesized. In some embodiments, the chemical synthesis uses automated, solid-phase oligonucleotide synthesis machines with 2′-acetoxyethyl orthoester (2′-ACE) (Scaringe et al., J. Am. Chem. Soc. (1998) 120: 11820-11821; Scaringe, Methods Enzymol. (2000) 317: 3-18) or 2′-thionocarbamate (2′-TC) chemistry (Dellinger et al., J. Am. Chem. Soc. (2011) 133: 11540-11546; Hendel et al., Nat. Biotechnol. (2015) 33:985-989).

In certain embodiments, the guide molecule comprises (1) a guide sequence capable of hybridizing to a target locus and (2) a tracr mate or direct repeat sequence whereby the direct repeat sequence is located upstream (i.e., 5′) from the guide sequence. In a particular embodiment the seed sequence (i.e. the sequence essential critical for recognition and/or hybridization to the sequence at the target locus) of th guide sequence is approximately within the first 10 nucleotides of the guide sequence.

In a particular embodiment the guide molecule comprises a guide sequence linked to a direct repeat sequence, wherein the direct repeat sequence comprises one or more stem loops or optimized secondary structures. In particular embodiments, the direct repeat has a minimum length of 16 nts and a single stem loop. In further embodiments the direct repeat has a length longer than 16 nts, preferably more than 17 nts, and has more than one stem loops or optimized secondary structures. In particular embodiments the guide molecule comprises or consists of the guide sequence linked to all or part of the natural direct repeat sequence. A typical Type V or Type VI CRISPR-cas guide molecule comprises (in 3′ to 5′ direction or in 5′ to 3′ direction): a guide sequence a first complimentary stretch (the “repeat”), a loop (which is typically 4 or 5 nucleotides long), a second complimentary stretch (the “anti-repeat” being complimentary to the repeat), and a poly A (often poly U in RNA) tail (terminator). In certain embodiments, the direct repeat sequence retains its natural architecture and forms a single stem loop. In particular embodiments, certain aspects of the guide architecture can be modified, for example by addition, subtraction, or substitution of features, whereas certain other aspects of guide architecture are maintained. Preferred locations for engineered guide molecule modifications, including but not limited to insertions, deletions, and substitutions include guide termini and regions of the guide molecule that are exposed when complexed with the CRISPR-Cas protein and/or target, for example the stemloop of the direct repeat sequence.

In particular embodiments, the stem comprises at least about 4 bp comprising complementary X and Y sequences, although stems of more, e.g., 5, 6, 7, 8, 9, 10, 11 or 12 or fewer, e.g., 3, 2, base pairs are also contemplated. Thus, for example X2-10 and Y2-10 (wherein X and Y represent any complementary set of nucleotides) may be contemplated. In one aspect, the stem made of the X and Y nucleotides, together with the loop will form a complete hairpin in the overall secondary structure; and, this may be advantageous and the amount of base pairs can be any amount that forms a complete hairpin. In one aspect, any complementary X:Y basepairing sequence (e.g., as to length) is tolerated, so long as the secondary structure of the entire guide molecule is preserved. In one aspect, the loop that connects the stem made of X:Y basepairs can be any sequence of the same length (e.g., 4 or 5 nucleotides) or longer that does not interrupt the overall secondary structure of the guide molecule. In one aspect, the stemloop can further comprise, e.g. an MS2 aptamer. In one aspect, the stem comprises about 5-7 bp comprising complementary X and Y sequences, although stems of more or fewer basepairs are also contemplated. In one aspect, non-Watson Crick basepairing is contemplated, where such pairing otherwise generally preserves the architecture of the stemloop at that position.

In particular embodiments the natural hairpin or stemloop structure of the guide molecule is extended or replaced by an extended stemloop. It has been demonstrated that extension of the stem can enhance the assembly of the guide molecule with the CRISPR-Cas proten (Chen et al. Cell. (2013); 155(7): 1479-1491). In particular embodiments the stem of the stemloop is extended by at least 1, 2, 3, 4, 5 or more complementary basepairs (i.e. corresponding to the addition of 2,4, 6, 8, 10 or more nucleotides in the guide molecule). In particular embodiments these are located at the end of the stem, adjacent to the loop of the stemloop.

In particular embodiments, the susceptibility of the guide molecule to RNAses or to decreased expression can be reduced by slight modifications of the sequence of the guide molecule which do not affect its function. For instance, in particular embodiments, premature termination of transcription, such as premature transcription of U6 Pol-III, can be removed by modifying a putative Pol-III terminator (4 consecutive U's) in the guide molecules sequence. Where such sequence modification is required in the stemloop of the guide molecule, it is preferably ensured by a basepair flip.

In a particular embodiment the direct repeat may be modified to comprise one or more protein-binding RNA aptamers. In a particular embodiment, one or more aptamers may be included such as part of optimized secondary structure. Such aptamers may be capable of binding a bacteriophage coat protein as detailed further herein.

In some embodiments, the guide molecule forms a duplex with a target RNA comprising at least one target cytosine residue to be edited. Upon hybridization of the guide RNA molecule to the target RNA, the cytidine deaminase binds to the single strand RNA in the duplex made accessible by the mismatch in the guide sequence and catalyzes deamination of one or more target cytosine residues comprised within the stretch of mismatching nucleotides.

A guide sequence, and hence a nucleic acid-targeting guide RNA may be selected to target any target nucleic acid sequence. The target sequence may be mRNA.

In certain embodiments, the target sequence should be associated with a PAM (protospacer adjacent motif) or PFS (protospacer flanking sequence or site); that is, a short sequence recognized by the CRISPR complex. Depending on the nature of the CRISPR-Cas protein, the target sequence should be selected such that its complementary sequence in the DNA duplex (also referred to herein as the non-target sequence) is upstream or downstream of the PAM. In the embodiments of the present invention where the CRISPR-Cas protein is a Cas13 protein, the compelementary sequence of the target sequence is downstream or 3′ of the PAM or upstream or 5′ of the PAM. The precise sequence and length requirements for the PAM differ depending on the Cas13 protein used, but PAMs are typically 2-5 base pair sequences adjacent the protospacer (that is, the target sequence). Examples of the natural PAM sequences for different Cas13 orthologues are provided herein below and the skilled person will be able to identify further PAM sequences for use with a given Cas13 protein.

Further, engineering of the PAM Interacting (PI) domain may allow programming of PAM specificity, improve target site recognition fidelity, and increase the versatility of the CRISPR-Cas protein, for example as described for Cas9 in Kleinstiver B P et al. Engineered CRISPR-Cas9 nucleases with altered PAM specificities. Nature. 2015 Jul. 23; 523(7561):481-5. doi: 10.1038/nature14592. As further detailed herein, the skilled person will understand that Cas13 proteins may be modified analogously.

In particular embodiment, the guide is an escorted guide. By “escorted” is meant that the CRISPR-Cas system or complex or guide is delivered to a selected time or place within a cell, so that activity of the CRISPR-Cas system or complex or guide is spatially or temporally controlled. For example, the activity and destination of the 3 CRISPR-Cas system or complex or guide may be controlled by an escort RNA aptamer sequence that has binding affinity for an aptamer ligand, such as a cell surface protein or other localized cellular component. Alternatively, the escort aptamer may for example be responsive to an aptamer effector on or in the cell, such as a transient effector, such as an external energy source that is applied to the cell at a particular time.

The escorted CRISPR-Cas systems or complexes have a guide molecule with a functional structure designed to improve guide molecule structure, architecture, stability, genetic expression, or any combination thereof. Such a structure can include an aptamer.

Aptamers are biomolecules that can be designed or selected to bind tightly to other ligands, for example using a technique called systematic evolution of ligands by exponential enrichment (SELEX; Tuerk C, Gold L: “Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase.” Science 1990, 249:505-510). Nucleic acid aptamers can for example be selected from pools of random-sequence oligonucleotides, with high binding affinities and specificities for a wide range of biomedically relevant targets, suggesting a wide range of therapeutic utilities for aptamers (Keefe, Anthony D., Supriya Pai, and Andrew Ellington. “Aptamers as therapeutics.” Nature Reviews Drug Discovery 9.7 (2010): 537-550). These characteristics also suggest a wide range of uses for aptamers as drug delivery vehicles (Levy-Nissenbaum, Etgar, et al. “Nanotechnology and aptamers: applications in drug delivery.” Trends in biotechnology 26.8 (2008): 442-449; and, Hicke B J, Stephens A W. “Escort aptamers: a delivery service for diagnosis and therapy.” J Clin Invest 2000, 106:923-928.). Aptamers may also be constructed that function as molecular switches, responding to a que by changing properties, such as RNA aptamers that bind fluorophores to mimic the activity of green flourescent protein (Paige, Jeremy S., Karen Y. Wu, and Samie R. Jaffrey. “RNA mimics of green fluorescent protein.” Science 333.6042 (2011): 642-646). It has also been suggested that aptamers may be used as components of targeted siRNA therapeutic delivery systems, for example targeting cell surface proteins (Zhou, Jiehua, and John J. Rossi. “Aptamer-targeted cell-specific RNA interference.” Silence 1.1 (2010): 4).

Accordingly, in particular embodiments, the guide molecule is modified, e.g., by one or more aptamer(s) designed to improve guide molecule delivery, including delivery across the cellular membrane, to intracellular compartments, or into the nucleus. Such a structure can include, either in addition to the one or more aptamer(s) or without such one or more aptamer(s), moiety(ies) so as to render the guide molecule deliverable, inducible or responsive to a selected effector. The invention accordingly comprehends an guide molecule that responds to normal or pathological physiological conditions, including without limitation pH, hypoxia, O₂ concentration, temperature, protein concentration, enzymatic concentration, lipid structure, light exposure, mechanical disruption (e.g. ultrasound waves), magnetic fields, electric fields, or electromagnetic radiation.

Light responsiveness of an inducible system may be achieved via the activation and binding of cryptochrome-2 and CIB 1. Blue light stimulation induces an activating conformational change in cryptochrome-2, resulting in recruitment of its binding partner CIB 1. This binding is fast and reversible, achieving saturation in <15 sec following pulsed stimulation and returning to baseline <15 min after the end of stimulation. These rapid binding kinetics result in a system temporally bound only by the speed of transcription/translation and transcript/protein degradation, rather than uptake and clearance of inducing agents. Crytochrome-2 activation is also highly sensitive, allowing for the use of low light intensity stimulation and mitigating the risks of phototoxicity. Further, in a context such as the intact mammalian brain, variable light intensity may be used to control the size of a stimulated region, allowing for greater precision than vector delivery alone may offer.

The invention contemplates energy sources such as electromagnetic radiation, sound energy or thermal energy to induce the guide. Advantageously, the electromagnetic radiation is a component of visible light. In a preferred embodiment, the light is a blue light with a wavelength of about 450 to about 495 nm. In an especially preferred embodiment, the wavelength is about 488 nm. In another preferred embodiment, the light stimulation is via pulses. The light power may range from about 0-9 mW/cm². In a preferred embodiment, a stimulation paradigm of as low as 0.25 sec every 15 sec should result in maximal activation.

The chemical or energy sensitive guide may undergo a conformational change upon induction by the binding of a chemical source or by the energy allowing it act as a guide and have the Cas13 CRISPR-Cas system or complex function. The invention can involve applying the chemical source or energy so as to have the guide function and the Cas13 CRISPR-Cas system or complex function; and optionally further determining that the expression of the genomic locus is altered.

There are several different designs of this chemical inducible system: 1. ABI-PYL based system inducible by Abscisic Acid (ABA) (see, e.g., stke.sciencemag.org/cgi/content/abstract/sigtrans;4/164/rs2), 2. FKBP-FRB based system inducible by rapamycin (or related chemicals based on rapamycin) (see, e.g., www.nature.com/nmeth/journal/v2/n6/full/nmeth763.html), 3. GID1-GAI based system inducible by Gibberellin (GA) (see, e.g., www.nature.com/nchembio/journal/v8/n5/full/nchembio.922.html).

A chemical inducible system can be an estrogen receptor (ER) based system inducible by 4-hydroxytamoxifen (4OHT) (see, e.g., www.pnas.org/content/104/3/1027.abstract). A mutated ligand-binding domain of the estrogen receptor called ERT2 translocates into the nucleus of cells upon binding of 4-hydroxytamoxifen. In further embodiments of the invention any naturally occurring or engineered derivative of any nuclear receptor, thyroid hormone receptor, retinoic acid receptor, estrogren receptor, estrogen-related receptor, glucocorticoid receptor, progesterone receptor, androgen receptor may be used in inducible systems analogous to the ER based inducible system.

Another inducible system is based on the design using Transient receptor potential (TRP) ion channel based system inducible by energy, heat or radio-wave (see, e.g., www.sciencemag.org/content/336/6081/604). These TRP family proteins respond to different stimuli, including light and heat. When this protein is activated by light or heat, the ion channel will open and allow the entering of ions such as calcium into the plasma membrane. This influx of ions will bind to intracellular ion interacting partners linked to a polypeptide including the guide and the other components of the Cas13 CRISPR-Cas complex or system, and the binding will induce the change of sub-cellular localization of the polypeptide, leading to the entire polypeptide entering the nucleus of cells. Once inside the nucleus, the guide protein and the other components of the Cas13 CRISPR-Cas complex will be active and modulating target gene expression in cells.

While light activation may be an advantageous embodiment, sometimes it may be disadvantageous especially for in vivo applications in which the light may not penetrate the skin or other organs. In this instance, other methods of energy activation are contemplated, in particular, electric field energy and/or ultrasound which have a similar effect.

Electric field energy is preferably administered substantially as described in the art, using one or more electric pulses of from about 1 Volt/cm to about 10 kVolts/cm under in vivo conditions. Instead of or in addition to the pulses, the electric field may be delivered in a continuous manner. The electric pulse may be applied for between 1 μs and 500 milliseconds, preferably between 1 μs and 100 milliseconds. The electric field may be applied continuously or in a pulsed manner for 5 about minutes.

As used herein, ‘electric field energy’ is the electrical energy to which a cell is exposed. Preferably the electric field has a strength of from about 1 Volt/cm to about 10 kVolts/cm or more under in vivo conditions (see WO97/49450).

As used herein, the term “electric field” includes one or more pulses at variable capacitance and voltage and including exponential and/or square wave and/or modulated wave and/or modulated square wave forms. References to electric fields and electricity should be taken to include reference the presence of an electric potential difference in the environment of a cell. Such an environment may be set up by way of static electricity, alternating current (AC), direct current (DC), etc, as known in the art. The electric field may be uniform, non-uniform or otherwise, and may vary in strength and/or direction in a time dependent manner.

Single or multiple applications of electric field, as well as single or multiple applications of ultrasound are also possible, in any order and in any combination. The ultrasound and/or the electric field may be delivered as single or multiple continuous applications, or as pulses (pulsatile delivery).

Electroporation has been used in both in vitro and in vivo procedures to introduce foreign material into living cells. With in vitro applications, a sample of live cells is first mixed with the agent of interest and placed between electrodes such as parallel plates. Then, the electrodes apply an electrical field to the cell/implant mixture. Examples of systems that perform in vitro electroporation include the Electro Cell Manipulator ECM600 product, and the Electro Square Porator T820, both made by the BTX Division of Genetronics, Inc (see U.S. Pat. No. 5,869,326).

The known electroporation techniques (both in vitro and in vivo) function by applying a brief high voltage pulse to electrodes positioned around the treatment region. The electric field generated between the electrodes causes the cell membranes to temporarily become porous, whereupon molecules of the agent of interest enter the cells. In known electroporation applications, this electric field comprises a single square wave pulse on the order of 1000 V/cm, of about 100 .mu.s duration. Such a pulse may be generated, for example, in known applications of the Electro Square Porator T820.

Preferably, the electric field has a strength of from about 1 V/cm to about 10 kV/cm under in vitro conditions. Thus, the electric field may have a strength of 1 V/cm, 2 V/cm, 3 V/cm, 4 V/cm, 5 V/cm, 6 V/cm, 7 V/cm, 8 V/cm, 9 V/cm, 10 V/cm, 20 V/cm, 50 V/cm, 100 V/cm, 200 V/cm, 300 V/cm, 400 V/cm, 500 V/cm, 600 V/cm, 700 V/cm, 800 V/cm, 900 V/cm, 1 kV/cm, 2 kV/cm, 5 kV/cm, 10 kV/cm, 20 kV/cm, 50 kV/cm or more. More preferably from about 0.5 kV/cm to about 4.0 kV/cm under in vitro conditions. Preferably the electric field has a strength of from about 1 V/cm to about 10 kV/cm under in vivo conditions. However, the electric field strengths may be lowered where the number of pulses delivered to the target site are increased. Thus, pulsatile delivery of electric fields at lower field strengths is envisaged.

Preferably the application of the electric field is in the form of multiple pulses such as double pulses of the same strength and capacitance or sequential pulses of varying strength and/or capacitance. As used herein, the term “pulse” includes one or more electric pulses at variable capacitance and voltage and including exponential and/or square wave and/or modulated wave/square wave forms.

Preferably the electric pulse is delivered as a waveform selected from an exponential wave form, a square wave form, a modulated wave form and a modulated square wave form.

A preferred embodiment employs direct current at low voltage. Thus, Applicants disclose the use of an electric field which is applied to the cell, tissue or tissue mass at a field strength of between 1V/cm and 20V/cm, for a period of 100 milliseconds or more, preferably 15 minutes or more.

Ultrasound is advantageously administered at a power level of from about 0.05 W/cm2 to about 100 W/cm2. Diagnostic or therapeutic ultrasound may be used, or combinations thereof.

As used herein, the term “ultrasound” refers to a form of energy which consists of mechanical vibrations the frequencies of which are so high they are above the range of human hearing. Lower frequency limit of the ultrasonic spectrum may generally be taken as about 20 kHz. Most diagnostic applications of ultrasound employ frequencies in the range 1 and 15 MHz' (From Ultrasonics in Clinical Diagnosis, P. N. T. Wells, ed., 2nd. Edition, Publ. Churchill Livingstone [Edinburgh, London & NY, 1977]).

Ultrasound has been used in both diagnostic and therapeutic applications. When used as a diagnostic tool (“diagnostic ultrasound”), ultrasound is typically used in an energy density range of up to about 100 mW/cm2 (FDA recommendation), although energy densities of up to 750 mW/cm2 have been used. In physiotherapy, ultrasound is typically used as an energy source in a range up to about 3 to 4 W/cm2 (WHO recommendation). In other therapeutic applications, higher intensities of ultrasound may be employed, for example, HIFU at 100 W/cm up to 1 kW/cm2 (or even higher) for short periods of time. The term “ultrasound” as used in this specification is intended to encompass diagnostic, therapeutic and focused ultrasound.

Focused ultrasound (FUS) allows thermal energy to be delivered without an invasive probe (see Morocz et al 1998 Journal of Magnetic Resonance Imaging Vol. 8, No. 1, pp. 136-142. Another form of focused ultrasound is high intensity focused ultrasound (HIFU) which is reviewed by Moussatov et al in Ultrasonics (1998) Vol. 36, No. 8, pp. 893-900 and TranHuuHue et al in Acustica (1997) Vol. 83, No. 6, pp. 1103-1106.

Preferably, a combination of diagnostic ultrasound and a therapeutic ultrasound is employed. This combination is not intended to be limiting, however, and the skilled reader will appreciate that any variety of combinations of ultrasound may be used. Additionally, the energy density, frequency of ultrasound, and period of exposure may be varied.

Preferably the exposure to an ultrasound energy source is at a power density of from about 0.05 to about 100 Wcm-2. Even more preferably, the exposure to an ultrasound energy source is at a power density of from about 1 to about 15 Wcm-2.

Preferably the exposure to an ultrasound energy source is at a frequency of from about 0.015 to about 10.0 MHz. More preferably the exposure to an ultrasound energy source is at a frequency of from about 0.02 to about 5.0 MHz or about 6.0 MHz. Most preferably, the ultrasound is applied at a frequency of 3 MHz.

Preferably the exposure is for periods of from about 10 milliseconds to about 60 minutes. Preferably the exposure is for periods of from about 1 second to about 5 minutes. More preferably, the ultrasound is applied for about 2 minutes. Depending on the particular target cell to be disrupted, however, the exposure may be for a longer duration, for example, for 15 minutes.

Advantageously, the target tissue is exposed to an ultrasound energy source at an acoustic power density of from about 0.05 Wcm-2 to about 10 Wcm-2 with a frequency ranging from about 0.015 to about 10 MHz (see WO 98/52609). However, alternatives are also possible, for example, exposure to an ultrasound energy source at an acoustic power density of above 100 Wcm-2, but for reduced periods of time, for example, 1000 Wcm-2 for periods in the millisecond range or less.

Preferably the application of the ultrasound is in the form of multiple pulses; thus, both continuous wave and pulsed wave (pulsatile delivery of ultrasound) may be employed in any combination. For example, continuous wave ultrasound may be applied, followed by pulsed wave ultrasound, or vice versa. This may be repeated any number of times, in any order and combination. The pulsed wave ultrasound may be applied against a background of continuous wave ultrasound, and any number of pulses may be used in any number of groups.

Preferably, the ultrasound may comprise pulsed wave ultrasound. In a highly preferred embodiment, the ultrasound is applied at a power density of 0.7 Wcm-2 or 1.25 Wcm-2 as a continuous wave. Higher power densities may be employed if pulsed wave ultrasound is used.

Use of ultrasound is advantageous as, like light, it may be focused accurately on a target. Moreover, ultrasound is advantageous as it may be focused more deeply into tissues unlike light. It is therefore better suited to whole-tissue penetration (such as but not limited to a lobe of the liver) or whole organ (such as but not limited to the entire liver or an entire muscle, such as the heart) therapy. Another important advantage is that ultrasound is a non-invasive stimulus which is used in a wide variety of diagnostic and therapeutic applications. By way of example, ultrasound is well known in medical imaging techniques and, additionally, in orthopedic therapy. Furthermore, instruments suitable for the application of ultrasound to a subject vertebrate are widely available and their use is well known in the art.

In particular embodiments, the guide molecule is modified by a secondary structure to increase the specificity of the CRISPR-Cas system and the secondary structure can protect against exonuclease activity and allow for 5′ additions to the guide sequence also referred to herein as a protected guide molecule.

In one aspect, the invention provides for hybridizing a “protector RNA” to a sequence of the guide molecule, wherein the “protector RNA” is an RNA strand complementary to the 3′ end of the guide molecule to thereby generate a partially double-stranded guide RNA. In an embodiment of the invention, protecting mismatched bases (i.e. the bases of the guide molecule which do not form part of the guide sequence) with a perfectly complementary protector sequence decreases the likelihood of target RNA binding to the mismatched basepairs at the 3′ end. In particular embodiments of the invention, additional sequences comprising an extented length may also be present within the guide molecule such that the guide comprises a protector sequence within the guide molecule. This “protector sequence” ensures that the guide molecule comprises a “protected sequence” in addition to an “exposed sequence” (comprising the part of the guide sequence hybridizing to the target sequence). In particular embodiments, the guide molecule is modified by the presence of the protector guide to comprise a secondary structure such as a hairpin. Advantageously there are three or four to thirty or more, e.g., about 10 or more, contiguous base pairs having complementarity to the protected sequence, the guide sequence or both. It is advantageous that the protected portion does not impede thermodynamics of the CRISPR-Cas system interacting with its target. By providing such an extension including a partially double stranded guide moleucle, the guide molecule is considered protected and results in improved specific binding of the CRISPR-Cas complex, while maintaining specific activity.

In particular embodiments, use is made of a truncated guide (tru-guide), i.e. a guide molecule which comprises a guide sequence which is truncated in length with respect to the canonical guide sequence length. As described by Nowak et al. (Nucleic Acids Res (2016) 44 (20): 9555-9564), such guides may allow catalytically active CRISPR-Cas enzyme to bind its target without cleaving the target RNA. In particular embodiments, a truncated guide is used which allows the binding of the target but retains only nickase activity of the CRISPR-Cas enzyme.

The present invention may be further illustrated and extended based on aspects of CRISPR-Cas development and use as set forth in the following articles and particularly as relates to delivery of a CRISPR protein complex and uses of an RNA guided endonuclease in cells and organisms:

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Epub 2015 Sep. 16.     -   Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas         System, Zetsche et al., Cell 163, 759-71 (Sep. 25, 2015).     -   Discovery and Functional Characterization of Diverse Class 2         CRISPR-Cas Systems, Shmakov et al., Molecular Cell, 60(3),         385-397 doi: 10.1016/j.molcel.2015.10.008 Epub Oct. 22, 2015.     -   Rationally engineered Cas9 nucleases with improved specificity,         Slaymaker et al., Science 2016 Jan. 1 351(6268): 84-88 doi:         10.1126/science.aad5227. Epub 2015 Dec. 1.     -   Gao et al, “Engineered Cpf1 Enzymes with Altered PAM         Specificities,” bioRxiv 091611; doi:         http://dx.doi.org/10.1101/091611 (Dec. 4, 2016).

each of which is incorporated herein by reference, may be considered in the practice of the instant invention, and discussed briefly below:

-   -   Cong et at. engineered type II CRISPR-Cas systems for use in         eukaryotic cells based on both Streptococcus thermophilus Cas9         and also Streptococcus pyogenes Cas9 and demonstrated that Cas9         nucleases can be directed by short RNAs to induce precise         cleavage of DNA in human and mouse cells. Their study further         showed that Cas9 as converted into a nicking enzyme can be used         to facilitate homology-directed repair in eukaryotic cells with         minimal mutagenic activity. Additionally, their study         demonstrated that multiple guide sequences can be encoded into a         single CRISPR array to enable simultaneous editing of several at         endogenous genomic loci sites within the mammalian genome,         demonstrating easy programmability and wide applicability of the         RNA-guided nuclease technology. This ability to use RNA to         program sequence specific DNA cleavage in cells defined a new         class of genome engineering tools. These studies further showed         that other CRISPR loci are likely to be transplantable into         mammalian cells and can also mediate mammalian genome cleavage.         Importantly, it can be envisaged that several aspects of the         CRISPR-Cas system can be further improved to increase its         efficiency and versatility.     -   Jiang et al. used the clustered, regularly interspaced, short         palindromic repeats (CRISPR)-associated Cas9 endonuclease         complexed with dual-RNAs to introduce precise mutations in the         genomes of Streptococcus pneumoniae and Escherichia coli. The         approach relied on dual-RNA:Cas9-directed cleavage at the         targeted genomic site to kill unmutated cells and circumvents         the need for selectable markers or counter-selection systems.         The study reported reprogramming dual-RNA:Cas9 specificity by         changing the sequence of short CRISPR RNA (crRNA) to make         single- and multinucleotide changes carried on editing         templates. The study showed that simultaneous use of two crRNAs         enabled multiplex mutagenesis. Furthermore, when the approach         was used in combination with recombineering, in S. pneumoniae,         nearly 100% of cells that were recovered using the described         approach contained the desired mutation, and in E. coli, 65%         that were recovered contained the mutation.     -   Wang et al. (2013) used the CRISPR-Cas system for the one-step         generation of mice carrying mutations in multiple genes which         were traditionally generated in multiple steps by sequential         recombination in embryonic stem cells and/or time-consuming         intercrossing of mice with a single mutation. The CRISPR-Cas         system will greatly accelerate the in vivo study of functionally         redundant genes and of epistatic gene interactions.     -   Konermann et al. (2013) addressed the need in the art for         versatile and robust technologies that enable optical and         chemical modulation of DNA-binding domains based CRISPR Cas9         enzyme and also Transcriptional Activator Like Effectors     -   Ran et al. (2013-A) described an approach that combined a Cas9         nickase mutant with paired guide RNAs to introduce targeted         double-strand breaks. This addresses the issue of the Cas9         nuclease from the microbial CRISPR-Cas system being targeted to         specific genomic loci by a guide sequence, which can tolerate         certain mismatches to the DNA target and thereby promote         undesired off-target mutagenesis. Because individual nicks in         the genome are repaired with high fidelity, simultaneous nicking         via appropriately offset guide RNAs is required for         double-stranded breaks and extends the number of specifically         recognized bases for target cleavage. The authors demonstrated         that using paired nicking can reduce off-target activity by 50-         to 1,500-fold in cell lines and to facilitate gene knockout in         mouse zygotes without sacrificing on-target cleavage efficiency.         This versatile strategy enables a wide variety of genome editing         applications that require high specificity.     -   Hsu et al. (2013) characterized SpCas9 targeting specificity in         human cells to inform the selection of target sites and avoid         off-target effects. The study evaluated >700 guide RNA variants         and SpCas9-induced indel mutation levels at >100 predicted         genomic off-target loci in 293T and 293FT cells. The authors         that SpCas9 tolerates mismatches between guide RNA and target         DNA at different positions in a sequence-dependent manner,         sensitive to the number, position and distribution of         mismatches. The authors further showed that SpCas9-mediated         cleavage is unaffected by DNA methylation and that the dosage of         SpCas9 and guide RNA can be titrated to minimize off-target         modification. Additionally, to facilitate mammalian genome         engineering applications, the authors reported providing a         web-based software tool to guide the selection and validation of         target sequences as well as off-target analyses.     -   Ran et al. (2013-B) described a set of tools for Cas9-mediated         genome editing via non-homologous end joining (NHEJ) or         homology-directed repair (HDR) in mammalian cells, as well as         generation of modified cell lines for downstream functional         studies. To minimize off-target cleavage, the authors further         described a double-nicking strategy using the Cas9 nickase         mutant with paired guide RNAs. The protocol provided by the         authors experimentally derived guidelines for the selection of         target sites, evaluation of cleavage efficiency and analysis of         off-target activity. The studies showed that beginning with         target design, gene modifications can be achieved within as         little as 1-2 weeks, and modified clonal cell lines can be         derived within 2-3 weeks.     -   Shalem et al. described a new way to interrogate gene function         on a genome-wide scale. Their studies showed that delivery of a         genome-scale CRISPR-Cas9 knockout (GeCKO) library targeted         18,080 genes with 64,751 unique guide sequences enabled both         negative and positive selection screening in human cells. First,         the authors showed use of the GeCKO library to identify genes         essential for cell viability in cancer and pluripotent stem         cells. Next, in a melanoma model, the authors screened for genes         whose loss is involved in resistance to vemurafenib, a         therapeutic that inhibits mutant protein kinase BRAF. Their         studies showed that the highest-ranking candidates included         previously validated genes NF1 and MED12 as well as novel hits         NF2, CUL3, TADA2B, and TADA1. The authors observed a high level         of consistency between independent guide RNAs targeting the same         gene and a high rate of hit confirmation, and thus demonstrated         the promise of genome-scale screening with Cas9.     -   Nishimasu et al. reported the crystal structure of Streptococcus         pyogenes Cas9 in complex with sgRNA and its target DNA at 2.5 A°         resolution. The structure revealed a bilobed architecture         composed of target recognition and nuclease lobes, accommodating         the sgRNA:DNA heteroduplex in a positively charged groove at         their interface. Whereas the recognition lobe is essential for         binding sgRNA and DNA, the nuclease lobe contains the HNH and         RuvC nuclease domains, which are properly positioned for         cleavage of the complementary and non-complementary strands of         the target DNA, respectively. The nuclease lobe also contains a         carboxyl-terminal domain responsible for the interaction with         the protospacer adjacent motif (PAM). This high-resolution         structure and accompanying functional analyses have revealed the         molecular mechanism of RNA-guided DNA targeting by Cas9, thus         paving the way for the rational design of new, versatile         genome-editing technologies.     -   Wu et al. mapped genome-wide binding sites of a catalytically         inactive Cas9 (dCas9) from Streptococcus pyogenes loaded with         single guide RNAs (sgRNAs) in mouse embryonic stem cells         (mESCs). The authors showed that each of the four sgRNAs tested         targets dCas9 to between tens and thousands of genomic sites,         frequently characterized by a 5-nucleotide seed region in the         sgRNA and an NGG protospacer adjacent motif (PAM). Chromatin         inaccessibility decreases dCas9 binding to other sites with         matching seed sequences; thus 70% of off-target sites are         associated with genes. The authors showed that targeted         sequencing of 295 dCas9 binding sites in mESCs transfected with         catalytically active Cas9 identified only one site mutated above         background levels. The authors proposed a two-state model for         Cas9 binding and cleavage, in which a seed match triggers         binding but extensive pairing with target DNA is required for         cleavage.     -   Platt et al. established a Cre-dependent Cas9 knockin mouse. The         authors demonstrated in vivo as well as ex vivo genome editing         using adeno-associated virus (AAV)-, lentivirus-, or         particle-mediated delivery of guide RNA in neurons, immune         cells, and endothelial cells.     -   Hsu et al. (2014) is a review article that discusses generally         CRISPR-Cas9 history from yogurt to genome editing, including         genetic screening of cells.     -   Wang et al. (2014) relates to a pooled, loss-of-function genetic         screening approach suitable for both positive and negative         selection that uses a genome-scale lentiviral single guide RNA         (sgRNA) library.     -   Doench et al. created a pool of sgRNAs, tiling across all         possible target sites of a panel of six endogenous mouse and         three endogenous human genes and quantitatively assessed their         ability to produce null alleles of their target gene by antibody         staining and flow cytometry. The authors showed that         optimization of the PAM improved activity and also provided an         on-line tool for designing sgRNAs.     -   Swiech et al. demonstrate that AAV-mediated SpCas9 genome         editing can enable reverse genetic studies of gene function in         the brain.     -   Konermann et al. (2015) discusses the ability to attach multiple         effector domains, e.g., transcriptional activator, functional         and epigenomic regulators at appropriate positions on the guide         such as stem or tetraloop with and without linkers.     -   Zetsche et al. demonstrates that the Cas9 enzyme can be split         into two and hence the assembly of Cas9 for activation can be         controlled.     -   Chen et al. relates to multiplex screening by demonstrating that         a genome-wide in vivo CRISPR-Cas9 screen in mice reveals genes         regulating lung metastasis.     -   Ran et al. (2015) relates to SaCas9 and its ability to edit         genomes and demonstrates that one cannot extrapolate from         biochemical assays.     -   Shalem et al. (2015) described ways in which catalytically         inactive Cas9 (dCas9) fusions are used to synthetically repress         (CRISPRi) or activate (CRISPRa) expression, showing. advances         using Cas9 for genome-scale screens, including arrayed and         pooled screens, knockout approaches that inactivate genomic loci         and strategies that modulate transcriptional activity.     -   Xu et al. (2015) assessed the DNA sequence features that         contribute to single guide RNA (sgRNA) efficiency in         CRISPR-based screens. The authors explored efficiency of         CRISPR-Cas9 knockout and nucleotide preference at the cleavage         site. The authors also found that the sequence preference for         CRISPRi/a is substantially different from that for CRISPR-Cas9         knockout.     -   Parnas et al. (2015) introduced genome-wide pooled CRISPR-Cas9         libraries into dendritic cells (DCs) to identify genes that         control the induction of tumor necrosis factor (Tnf) by         bacterial lipopolysaccharide (LPS). Known regulators of Tlr4         signaling and previously unknown candidates were identified and         classified into three functional modules with distinct effects         on the canonical responses to LPS.     -   Ramanan et al (2015) demonstrated cleavage of viral episomal DNA         (cccDNA) in infected cells. The HBV genome exists in the nuclei         of infected hepatocytes as a 3.2kb double-stranded episomal DNA         species called covalently closed circular DNA (cccDNA), which is         a key component in the HBV life cycle whose replication is not         inhibited by current therapies. The authors showed that sgRNAs         specifically targeting highly conserved regions of HBV robustly         suppresses viral replication and depleted cccDNA.     -   Nishimasu et al. (2015) reported the crystal structures of         SaCas9 in complex with a single guide RNA (sgRNA) and its         double-stranded DNA targets, containing the 5′-TTGAAT-3′ PAM and         the 5′-TTGGGT-3′ PAM. A structural comparison of SaCas9 with         SpCas9 highlighted both structural conservation and divergence,         explaining their distinct PAM specificities and orthologous         sgRNA recognition.     -   Canver et al. (2015) demonstrated a CRISPR-Cas9-based functional         investigation of non-coding genomic elements. The authors we         developed pooled CRISPR-Cas9 guide RNA libraries to perform in         situ saturating mutagenesis of the human and mouse BCL11A         enhancers which revealed critical features of the enhancers.     -   Zetsche et al. (2015) reported characterization of Cpf1, a class         2 CRISPR nuclease from Francisella novicida U112 having features         distinct from Cas9. Cpf1 is a single RNA-guided endonuclease         lacking tracrRNA, utilizes a T-rich protospacer-adjacent motif,         and cleaves DNA via a staggered DNA double-stranded break.     -   Shmakov et al. (2015) reported three distinct Class 2 CRISPR-Cas         systems. Two system CRISPR enzymes (C2c1 and C2c3) contain         RuvC-like endonuclease domains distantly related to Cpf1. Unlike         Cpf1, C2c1 depends on both crRNA and tracrRNA for DNA cleavage.         The third enzyme (C2c2) contains two predicted HEPN RNase         domains and is tracrRNA independent.     -   Slaymaker et al (2016) reported the use of structure-guided         protein engineering to improve the specificity of Streptococcus         pyogenes Cas9 (SpCas9). The authors developed “enhanced         specificity” SpCas9 (eSpCas9) variants which maintained robust         on-target cleavage with reduced off-target effects.

The methods and tools provided herein are may be designed for use with or Cas13, a type II nuclease that does not make use of tracrRNA. Orthologs of Cas13 have been identified in different bacterial species as described herein. Further type II nucleases with similar properties can be identified using methods described in the art (Shmakov et al. 2015, 60:385-397; Abudayeh et al. 2016, Science, 5; 353(6299)). In particular embodiments, such methods for identifying novel CRISPR effector proteins may comprise the steps of selecting sequences from the database encoding a seed which identifies the presence of a CRISPR Cas locus, identifying loci located within 10 kb of the seed comprising Open Reading Frames (ORFs) in the selected sequences, selecting therefrom loci comprising ORFs of which only a single ORF encodes a novel CRISPR effector having greater than 700 amino acids and no more than 90% homology to a known CRISPR effector. In particular embodiments, the seed is a protein that is common to the CRISPR-Cas system, such as Cas1. In further embodiments, the CRISPR array is used as a seed to identify new effector proteins.

Also, “Dimeric CRISPR RNA-guided FokI nucleases for highly specific genome editing”, Shengdar Q. Tsai, Nicolas Wyvekens, Cyd Khayter, Jennifer A. Foden, Vishal Thapar, Deepak Reyon, Mathew J. Goodwin, Martin J. Aryee, J. Keith Joung Nature Biotechnology 32(6): 569-77 (2014), relates to dimeric RNA-guided FokIl Nucleases that recognize extended sequences and can edit endogenous genes with high efficiencies in human cells.

With respect to general information on CRISPR/Cas Systems, components thereof, and delivery of such components, including methods, materials, delivery vehicles, vectors, particles, and making and using thereof, including as to amounts and formulations, as well as CRISPR-Cas-expressing eukaryotic cells, CRISPR-Cas expressing eukaryotes, such as a mouse, reference is made to: U.S. Pat. Nos. 8,999,641, 8,993,233, 8,697,359, 8,771,945, 8,795,965, 8,865,406, 8,871,445, 8,889,356, 8,889,418, 8,895,308, 8,906,616, 8,932,814, and 8,945,839; US Patent Publications US 2014-0310830 (U.S. application Ser. No. 14/105,031), US 2014-0287938 A1 (U.S. application Ser. No. 14/213,991), US 2014-0273234 A1 (U.S. application Ser. No. 14/293,674), US2014-0273232 A1 (U.S. application Ser. No. 14/290,575), US 2014-0273231 (U.S. application Ser. No. 14/259,420), US 2014-0256046 A1 (U.S. application Ser. No. 14/226,274), US 2014-0248702 A1 (U.S. application Ser. No. 14/258,458), US 2014-0242700 A1 (U.S. application Ser. No. 14/222,930), US 2014-0242699 A1 (U.S. application Ser. No. 14/183,512), US 2014-0242664 A1 (U.S. application Ser. No. 14/104,990), US 2014-0234972 A1 (U.S. application Ser. No. 14/183,471), US 2014-0227787 A1 (U.S. application Ser. No. 14/256,912), US 2014-0189896 A1 (U.S. application Ser. No. 14/105,035), US 2014-0186958 (U.S. application Ser. No. 14/105,017), US 2014-0186919 A1 (U.S. application Ser. No. 14/104,977), US 2014-0186843 A1 (U.S. application Ser. No. 14/104,900), US 2014-0179770 A1 (U.S. application Ser. No. 14/104,837) and US 2014-0179006 A1 (U.S. application Ser. No. 14/183,486), US 2014-0170753 (U.S. application Ser. No. 14/183,429); US 2015-0184139 (U.S. application Ser. No. 14/324,960); Ser. No. 14/054,414 European Patent Applications EP 2 771 468 (EP13818570.7), EP 2 764 103 (EP13824232.6), and EP 2 784 162 (EP14170383.5); and PCT Patent Publications WO2014/093661 (PCT/US2013/074743), WO2014/093694 (PCT/US2013/074790), WO2014/093595 (PCT/US2013/074611), WO2014/093718 (PCT/US2013/074825), WO2014/093709 (PCT/US2013/074812), WO2014/093622 (PCT/US2013/074667), WO2014/093635 (PCT/US2013/074691), WO2014/093655 (PCT/US2013/074736), WO2014/093712 (PCT/US2013/074819), WO2014/093701 (PCT/US2013/074800), WO2014/018423 (PCT/US2013/051418), WO2014/204723 (PCT/US2014/041790), WO2014/204724 (PCT/US2014/041800), WO2014/204725 (PCT/US2014/041803), WO2014/204726 (PCT/US2014/041804), WO2014/204727 (PCT/US2014/041806), WO2014/204728 (PCT/US2014/041808), WO2014/204729 (PCT/US2014/041809), WO2015/089351 (PCT/US2014/069897), WO2015/089354 (PCT/US2014/069902), WO2015/089364 (PCT/US2014/069925), WO2015/089427 (PCT/US2014/070068), WO2015/089462 (PCT/US2014/070127), WO2015/089419 (PCT/US2014/070057), WO2015/089465 (PCT/US2014/070135), WO2015/089486 (PCT/US2014/070175), WO2015/058052 (PCT/US2014/061077), WO2015/070083 (PCT/US2014/064663), WO2015/089354 (PCT/US2014/069902), WO2015/089351 (PCT/US2014/069897), WO2015/089364 (PCT/US2014/069925), WO2015/089427 (PCT/US2014/070068), WO2015/089473 (PCT/US2014/070152), WO2015/089486 (PCT/US2014/070175), WO2016/049258 (PCT/US2015/051830), WO2016/094867 (PCT/US2015/065385), WO2016/094872 (PCT/US2015/065393), WO2016/094874 (PCT/US2015/065396), WO2016/106244 (PCT/US2015/067177).

Mention is also made of U.S. application 62/180,709, 17 Jun. 15, PROTECTED GUIDE RNAS (PGRNAS); U.S. application 62/091,455, filed, 12 Dec. 2014, PROTECTED GUIDE RNAS (PGRNAS); U.S. application 62/096,708, 24 Dec. 2014, PROTECTED GUIDE RNAS (PGRNAS); U.S. applications 62/091,462, 12 Dec. 2014, 62/096,324, 23 Dec. 2014, 62/180,681, 17 Jun. 2015, and 62/237,496, 5 Oct. 2015, DEAD GUIDES FOR CRISPR TRANSCRIPTION FACTORS; U.S. application 62/091,456, 12 Dec. 2014 and 62/180,692, 17 Jun. 2015, ESCORTED AND FUNCTIONALIZED GUIDES FOR CRISPR-CAS SYSTEMS; U.S. application 62/091,461, 12 Dec. 2014, DELIVERY, USE AND THERAPEUTIC APPLICATIONS OF THE CRISPR-CAS SYSTEMS AND COMPOSITIONS FOR GENOME EDITING AS TO HEMATOPOETIC STEM CELLS (HSCs); U.S. application 62/094,903, 19 Dec. 2014, UNBIASED IDENTIFICATION OF DOUBLE-STRAND BREAKS AND GENOMIC REARRANGEMENT BY GENOME-WISE INSERT CAPTURE SEQUENCING; U.S. application 62/096,761, 24 Dec. 2014, ENGINEERING OF SYSTEMS, METHODS AND OPTIMIZED ENZYME AND GUIDE SCAFFOLDS FOR SEQUENCE MANIPULATION; U.S. application 62/098,059, 30 Dec. 2014, 62/181,641, 18 Jun. 2015, and 62/181,667, 18 Jun. 2015, RNA-TARGETING SYSTEM; U.S. application 62/096,656, 24 Dec. 2014 and 62/181,151, 17 Jun. 2015, CRISPR HAVING OR ASSOCIATED WITH DESTABILIZATION DOMAINS; U.S. application 62/096,697, 24 Dec. 2014, CRISPR HAVING OR ASSOCIATED WITH AAV; U.S. application 62/098,158, 30 Dec. 2014, ENGINEERED CRISPR COMPLEX INSERTIONAL TARGETING SYSTEMS; U.S. application 62/151,052, 22 Apr. 2015, CELLULAR TARGETING FOR EXTRACELLULAR EXOSOMAL REPORTING; U.S. application 62/054,490, 24 Sep. 2014, DELIVERY, USE AND THERAPEUTIC APPLICATIONS OF THE CRISPR-CAS SYSTEMS AND COMPOSITIONS FOR TARGETING DISORDERS AND DISEASES USING PARTICLE DELIVERY COMPONENTS; U.S. application 61/939,154, 12 Feb. 2014, SYSTEMS, METHODS AND COMPOSITIONS FOR SEQUENCE MANIPULATION WITH OPTIMIZED FUNCTIONAL CRISPR-CAS SYSTEMS; U.S. application 62/055,484, 25 Sep. 2014, SYSTEMS, METHODS AND COMPOSITIONS FOR SEQUENCE MANIPULATION WITH OPTIMIZED FUNCTIONAL CRISPR-CAS SYSTEMS; U.S. application 62/087,537, 4 Dec. 2014, SYSTEMS, METHODS AND COMPOSITIONS FOR SEQUENCE MANIPULATION WITH OPTIMIZED FUNCTIONAL CRISPR-CAS SYSTEMS; U.S. application 62/054,651, 24 Sep. 2014, DELIVERY, USE AND THERAPEUTIC APPLICATIONS OF THE CRISPR-CAS SYSTEMS AND COMPOSITIONS FOR MODELING COMPETITION OF MULTIPLE CANCER MUTATIONS IN VIVO; U.S. application 62/067,886, 23 Oct. 2014, DELIVERY, USE AND THERAPEUTIC APPLICATIONS OF THE CRISPR-CAS SYSTEMS AND COMPOSITIONS FOR MODELING COMPETITION OF MULTIPLE CANCER MUTATIONS IN VIVO; U.S. applications 62/054,675, 24 Sep. 2014 and 62/181,002, 17 Jun. 2015, DELIVERY, USE AND THERAPEUTIC APPLICATIONS OF THE CRISPR-CAS SYSTEMS AND COMPOSITIONS IN NEURONAL CELLS/TISSUES; U.S. application 62/054,528, 24 Sep. 2014, DELIVERY, USE AND THERAPEUTIC APPLICATIONS OF THE CRISPR-CAS SYSTEMS AND COMPOSITIONS IN IMMUNE DISEASES OR DISORDERS; U.S. application 62/055,454, 25 Sep. 2014, DELIVERY, USE AND THERAPEUTIC APPLICATIONS OF THE CRISPR-CAS SYSTEMS AND COMPOSITIONS FOR TARGETING DISORDERS AND DISEASES USING CELL PENETRATION PEPTIDES (CPP); U.S. application 62/055,460, 25 Sep. 2014, MULTIFUNCTIONAL-CRISPR COMPLEXES AND/OR OPTIMIZED ENZYME LINKED FUNCTIONAL-CRISPR COMPLEXES; U.S. application 62/087,475, 4 Dec. 2014 and 62/181,690, 18 Jun. 2015, FUNCTIONAL SCREENING WITH OPTIMIZED FUNCTIONAL CRISPR-CAS SYSTEMS; U.S. application 62/055,487, 25 Sep. 2014, FUNCTIONAL SCREENING WITH OPTIMIZED FUNCTIONAL CRISPR-CAS SYSTEMS; U.S. application 62/087,546, 4 Dec. 2014 and 62/181,687, 18 Jun. 2015, MULTIFUNCTIONAL CRISPR COMPLEXES AND/OR OPTIMIZED ENZYME LINKED FUNCTIONAL-CRISPR COMPLEXES; and U.S. application 62/098,285, 30 Dec. 2014, CRISPR MEDIATED IN VIVO MODELING AND GENETIC SCREENING OF TUMOR GROWTH AND METASTASIS.

Mention is made of U.S. applications 62/181,659, 18 Jun. 2015 and 62/207,318, 19 Aug. 2015, ENGINEERING AND OPTIMIZATION OF SYSTEMS, METHODS, ENZYME AND GUIDE SCAFFOLDS OF CAS9 ORTHOLOGS AND VARIANTS FOR SEQUENCE MANIPULATION. Mention is made of U.S. applications 62/181,663, 18 Jun. 2015 and 62/245,264, 22 Oct. 2015, NOVEL CRISPR ENZYMES AND SYSTEMS, U.S. applications 62/181,675, 18 Jun. 2015, 62/285,349, 22 Oct. 2015, 62/296,522, 17 Feb. 2016, and 62/320,231, 8 Apr. 2016, NOVEL CRISPR ENZYMES AND SYSTEMS, U.S. application 62/232,067, 24 Sep. 2015, U.S. application Ser. No. 14/975,085, 18 Dec. 2015, European application No. 16150428.7, U.S. application 62/205,733, 16 Aug. 2015, U.S. application 62/201,542, 5 Aug. 2015, U.S. application 62/193,507, 16 Jul. 2015, and U.S. application 62/181,739, 18 Jun. 2015, each entitled NOVEL CRISPR ENZYMES AND SYSTEMS and of U.S. application 62/245,270, 22 Oct. 2015, NOVEL CRISPR ENZYMES AND SYSTEMS. Mention is also made of U.S. application 61/939,256, 12 Feb. 2014, and WO 2015/089473 (PCT/US2014/070152), 12 Dec. 2014, each entitled ENGINEERING OF SYSTEMS, METHODS AND OPTIMIZED GUIDE COMPOSITIONS WITH NEW ARCHITECTURES FOR SEQUENCE MANIPULATION. Mention is also made of PCT/US2015/045504, 15 Aug. 2015, U.S. application 62/180,699, 17 Jun. 2015, and U.S. application 62/038,358, 17 Aug. 2014, each entitled GENOME EDITING USING CAS9 NICKASES.

Each of these patents, patent publications, and applications, and all documents cited therein or during their prosecution (“appln cited documents”) and all documents cited or referenced in the appln cited documents, together with any instructions, descriptions, product specifications, and product sheets for any products mentioned therein or in any document therein and incorporated by reference herein, are hereby incorporated herein by reference, and may be employed in the practice of the invention. All documents (e.g., these patents, patent publications and applications and the appln cited documents) are incorporated herein by reference to the same extent as if each individual document was specifically and individually indicated to be incorporated by reference.

Tale Systems

As disclosed herein editing can be made by way of the transcription activator-like effector nucleases (TALENs) system. Transcription activator-like effectors (TALEs) can be engineered to bind practically any desired DNA sequence. Exemplary methods of genome editing using the TALEN system can be found for example in Cermak T. Doyle E L. Christian M. Wang L. Zhang Y. Schmidt C, et al. Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting. Nucleic Acids Res. 201 1; 39:e82; Zhang F. Cong L. Lodato S. Kosuri S. Church G M. Arlotta P Efficient construction of sequence-specific TAL effectors for modulating mammalian transcription. Nat Biotechnol. 2011; 29:149-153 and U.S. Pat. Nos. 8,450,471, 8,440,431 and 8,440,432, all of which are specifically incorporated by reference.

In advantageous embodiments of the invention, the methods provided herein use isolated, non-naturally occurring, recombinant or engineered DNA binding proteins that comprise TALE monomers as a part of their organizational structure that enable the targeting of nucleic acid sequences with improved efficiency and expanded specificity.

Naturally occurring TALEs or “wild type TALEs” are nucleic acid binding proteins secreted by numerous species of proteobacteria. TALE polypeptides contain a nucleic acid binding domain composed of tandem repeats of highly conserved monomer polypeptides that are predominantly 33, 34 or 35 amino acids in length and that differ from each other mainly in amino acid positions 12 and 13. In advantageous embodiments the nucleic acid is DNA. As used herein, the term “polypeptide monomers”, or “TALE monomers” will be used to refer to the highly conserved repetitive polypeptide sequences within the TALE nucleic acid binding domain and the term “repeat variable di-residues” or “RVD” will be used to refer to the highly variable amino acids at positions 12 and 13 of the polypeptide monomers. As provided throughout the disclosure, the amino acid residues of the RVD are depicted using the IUPAC single letter code for amino acids. A general representation of a TALE monomer which is comprised within the DNA binding domain is X1-11-(X12X13)-X14-33 or 34 or 35, where the subscript indicates the amino acid position and X represents any amino acid. X12X13 indicate the RVDs. In some polypeptide monomers, the variable amino acid at position 13 is missing or absent and in such polypeptide monomers, the RVD consists of a single amino acid. In such cases the RVD may be alternatively represented as X*, where X represents X12 and (*) indicates that X13 is absent. The DNA binding domain comprises several repeats of TALE monomers and this may be represented as (X1-11-(X12X13)-X14-33 or 34 or 35)z, where in an advantageous embodiment, z is at least 5 to 40. In a further advantageous embodiment, z is at least 10 to 26.

The TALE monomers have a nucleotide binding affinity that is determined by the identity of the amino acids in its RVD. For example, polypeptide monomers with an RVD of NI preferentially bind to adenine (A), polypeptide monomers with an RVD of NG preferentially bind to thymine (T), polypeptide monomers with an RVD of HD preferentially bind to cytosine (C) and polypeptide monomers with an RVD of NN preferentially bind to both adenine (A) and guanine (G). In yet another embodiment of the invention, polypeptide monomers with an RVD of IG preferentially bind to T. Thus, the number and order of the polypeptide monomer repeats in the nucleic acid binding domain of a TALE determines its nucleic acid target specificity. In still further embodiments of the invention, polypeptide monomers with an RVD of NS recognize all four base pairs and may bind to A, T, G or C. The structure and function of TALEs is further described in, for example, Moscou et al., Science 326:1501 (2009); Boch et al., Science 326:1509-1512 (2009); and Zhang et al., Nature Biotechnology 29:149-153 (2011), each of which is incorporated by reference in its entirety.

The TALE polypeptides used in methods of the invention are isolated, non-naturally occurring, recombinant or engineered nucleic acid-binding proteins that have nucleic acid or DNA binding regions containing polypeptide monomer repeats that are designed to target specific nucleic acid sequences.

As described herein, polypeptide monomers having an RVD of HN or NH preferentially bind to guanine and thereby allow the generation of TALE polypeptides with high binding specificity for guanine containing target nucleic acid sequences. In a preferred embodiment of the invention, polypeptide monomers having RVDs RN, NN, NK, SN, NH, KN, HN, NQ, HH, RG, KH, RH and SS preferentially bind to guanine. In a much more advantageous embodiment of the invention, polypeptide monomers having RVDs RN, NK, NQ, HH, KH, RH, SS and SN preferentially bind to guanine and thereby allow the generation of TALE polypeptides with high binding specificity for guanine containing target nucleic acid sequences. In an even more advantageous embodiment of the invention, polypeptide monomers having RVDs HH, KH, NH, NK, NQ, RH, RN and SS preferentially bind to guanine and thereby allow the generation of TALE polypeptides with high binding specificity for guanine containing target nucleic acid sequences. In a further advantageous embodiment, the RVDs that have high binding specificity for guanine are RN, NH RH and KH. Furthermore, polypeptide monomers having an RVD of NV preferentially bind to adenine and guanine. In more preferred embodiments of the invention, polypeptide monomers having RVDs of H*, HA, KA, N*, NA, NC, NS, RA, and S* bind to adenine, guanine, cytosine and thymine with comparable affinity.

The predetermined N-terminal to C-terminal order of the one or more polypeptide monomers of the nucleic acid or DNA binding domain determines the corresponding predetermined target nucleic acid sequence to which the TALE polypeptides will bind. As used herein the polypeptide monomers and at least one or more half polypeptide monomers are “specifically ordered to target” the genomic locus or gene of interest. In plant genomes, the natural TALE-binding sites always begin with a thymine (T), which may be specified by a cryptic signal within the non-repetitive N-terminus of the TALE polypeptide; in some cases this region may be referred to as repeat 0. In animal genomes, TALE binding sites do not necessarily have to begin with a thymine (T) and TALE polypeptides may target DNA sequences that begin with T, A, G or C. The tandem repeat of TALE monomers always ends with a half-length repeat or a stretch of sequence that may share identity with only the first 20 amino acids of a repetitive full length TALE monomer and this half repeat may be referred to as a half-monomer (FIG. 8), which is included in the term “TALE monomer”. Therefore, it follows that the length of the nucleic acid or DNA being targeted is equal to the number of full polypeptide monomers plus two.

As described in Zhang et al., Nature Biotechnology 29:149-153 (2011), TALE polypeptide binding efficiency may be increased by including amino acid sequences from the “capping regions” that are directly N-terminal or C-terminal of the DNA binding region of naturally occurring TALEs into the engineered TALEs at positions N-terminal or C-terminal of the engineered TALE DNA binding region. Thus, in certain embodiments, the TALE polypeptides described herein further comprise an N-terminal capping region and/or a C-terminal capping region.

An exemplary amino acid sequence of a N-terminal capping region is:

(SEQ ID NO: 7) M D P I R S R T P S P A R E L L S G P Q P D G V Q P T A D R G V S P P A G G P L D G L P A R R T M S R T R L P S P P A P S P A F S A D S F S D L L R Q F D P S L F N T S L F D S L P P F G A H H T E A A T G E W D E V Q S G L R A A D A P P P T M R V A V T A A R P P R A K P A P R R R A A Q P S D A S P A A Q V D L R T L G Y S Q Q Q Q E K I K P K V R S T V A Q H H E A L V G H G F T H A H I V A L S Q H P A A L G T V A V K Y Q D M I A A L P E A T H E A I V G V G K Q W S G A R A L E A L L T V A G E L R G P P L Q L D T G Q L L K I A K R G G V T A V E A V H A W R N A L T G A P L N

An exemplary amino acid sequence of a C-terminal capping region is:

(SEQ ID NO: 8) R P A L E S I V A Q L S R P D P A L A A L T N D H L V A L A C L G G R P A L D A V K K G L P H A P A L I K R T N R R I P E R T S H R V A D H A Q V V R V L G F F Q C H S H P A Q A F D D A M T Q F G M S R H G L L Q L F R R V G V T E L E A R S G T L P P A S Q R W D R I L Q A S G M K R A K P S P T S T Q T P D Q A S L H A F A D S L E R D L D A P S P M H E G D Q T R A S 

As used herein the predetermined “N-terminus” to “C terminus” orientation of the N-terminal capping region, the DNA binding domain comprising the repeat TALE monomers and the C-terminal capping region provide structural basis for the organization of different domains in the d-TALEs or polypeptides of the invention.

The entire N-terminal and/or C-terminal capping regions are not necessary to enhance the binding activity of the DNA binding region. Therefore, in certain embodiments, fragments of the N-terminal and/or C-terminal capping regions are included in the TALE polypeptides described herein.

In certain embodiments, the TALE polypeptides described herein contain a N-terminal capping region fragment that included at least 10, 20, 30, 40, 50, 54, 60, 70, 80, 87, 90, 94, 100, 102, 110, 117, 120, 130, 140, 147, 150, 160, 170, 180, 190, 200, 210, 220, 230, 240, 250, 260 or 270 amino acids of an N-terminal capping region. In certain embodiments, the N-terminal capping region fragment amino acids are of the C-terminus (the DNA-binding region proximal end) of an N-terminal capping region. As described in Zhang et al., Nature Biotechnology 29:149-153 (2011), N-terminal capping region fragments that include the C-terminal 240 amino acids enhance binding activity equal to the full length capping region, while fragments that include the C-terminal 147 amino acids retain greater than 80% of the efficacy of the full length capping region, and fragments that include the C-terminal 117 amino acids retain greater than 50% of the activity of the full-length capping region.

In some embodiments, the TALE polypeptides described herein contain a C-terminal capping region fragment that included at least 6, 10, 20, 30, 37, 40, 50, 60, 68, 70, 80, 90, 100, 110, 120, 127, 130, 140, 150, 155, 160, 170, 180 amino acids of a C-terminal capping region. In certain embodiments, the C-terminal capping region fragment amino acids are of the N-terminus (the DNA-binding region proximal end) of a C-terminal capping region. As described in Zhang et al., Nature Biotechnology 29:149-153 (2011), C-terminal capping region fragments that include the C-terminal 68 amino acids enhance binding activity equal to the full length capping region, while fragments that include the C-terminal 20 amino acids retain greater than 50% of the efficacy of the full length capping region.

In certain embodiments, the capping regions of the TALE polypeptides described herein do not need to have identical sequences to the capping region sequences provided herein. Thus, in some embodiments, the capping region of the TALE polypeptides described herein have sequences that are at least 50%, 60%, 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical or share identity to the capping region amino acid sequences provided herein. Sequence identity is related to sequence homology. Homology comparisons may be conducted by eye, or more usually, with the aid of readily available sequence comparison programs. These commercially available computer programs may calculate percent (%) homology between two or more sequences and may also calculate the sequence identity shared by two or more amino acid or nucleic acid sequences. In some preferred embodiments, the capping region of the TALE polypeptides described herein have sequences that are at least 95% identical or share identity to the capping region amino acid sequences provided herein.

Sequence homologies may be generated by any of a number of computer programs known in the art, which include but are not limited to BLAST or FASTA. Suitable computer program for carrying out alignments like the GCG Wisconsin Bestfit package may also be used. Once the software has produced an optimal alignment, it is possible to calculate % homology, preferably % sequence identity. The software typically does this as part of the sequence comparison and generates a numerical result.

In advantageous embodiments described herein, the TALE polypeptides of the invention include a nucleic acid binding domain linked to the one or more effector domains. The terms “effector domain” or “regulatory and functional domain” refer to a polypeptide sequence that has an activity other than binding to the nucleic acid sequence recognized by the nucleic acid binding domain. By combining a nucleic acid binding domain with one or more effector domains, the polypeptides of the invention may be used to target the one or more functions or activities mediated by the effector domain to a particular target DNA sequence to which the nucleic acid binding domain specifically binds.

In some embodiments of the TALE polypeptides described herein, the activity mediated by the effector domain is a biological activity. For example, in some embodiments the effector domain is a transcriptional inhibitor (i.e., a repressor domain), such as an mSin interaction domain (SID). SID4X domain or a Kruppel-associated box (KRAB) or fragments of the KRAB domain. In some embodiments the effector domain is an enhancer of transcription (i.e. an activation domain), such as the VP16, VP64 or p65 activation domain. In some embodiments, the nucleic acid binding is linked, for example, with an effector domain that includes but is not limited to a transposase, integrase, recombinase, resolvase, invertase, protease, DNA methyltransferase, DNA demethylase, histone acetylase, histone deacetylase, nuclease, transcriptional repressor, transcriptional activator, transcription factor recruiting, protein nuclear-localization signal or cellular uptake signal.

In some embodiments, the effector domain is a protein domain which exhibits activities which include but are not limited to transposase activity, integrase activity, recombinase activity, resolvase activity, invertase activity, protease activity, DNA methyltransferase activity, DNA demethylase activity, histone acetylase activity, histone deacetylase activity, nuclease activity, nuclear-localization signaling activity, transcriptional repressor activity, transcriptional activator activity, transcription factor recruiting activity, or cellular uptake signaling activity. Other preferred embodiments of the invention may include any combination the activities described herein.

ZN-Finger Nucleases

Other preferred tools for genome editing for use in the context of this invention include zinc finger systems and TALE systems. One type of programmable DNA-binding domain is provided by artificial zinc-finger (ZF) technology, which involves arrays of ZF modules to target new DNA-binding sites in the genome. Each finger module in a ZF array targets three DNA bases. A customized array of individual zinc finger domains is assembled into a ZF protein (ZFP).

ZFPs can comprise a functional domain. The first synthetic zinc finger nucleases (ZFNs) were developed by fusing a ZF protein to the catalytic domain of the Type IIS restriction enzyme FokI. (Kim, Y. G. et al., 1994, Chimeric restriction endonuclease, Proc. Natl. Acad. Sci. U.S.A. 91, 883-887; Kim, Y. G. et al., 1996, Hybrid restriction enzymes: zinc finger fusions to Fok I cleavage domain. Proc. Natl. Acad. Sci. U.S.A. 93, 1156-1160). Increased cleavage specificity can be attained with decreased off target activity by use of paired ZFN heterodimers, each targeting different nucleotide sequences separated by a short spacer. (Doyon, Y. et al., 2011, Enhancing zinc-finger-nuclease activity with improved obligate heterodimeric architectures. Nat. Methods 8, 74-79). ZFPs can also be designed as transcription activators and repressors and have been used to target many genes in a wide variety of organisms.Exemplary methods of genome editing using ZFNs can be found for example in U.S. Pat. Nos. 6,534,261, 6,607,882, 6,746,838, 6,794,136, 6,824,978, 6,866,997, 6,933,113, 6,979,539, 7,013,219, 7,030,215, 7,220,719, 7,241,573, 7,241,574, 7,585,849, 7,595,376, 6,903,185, and 6,479,626, all of which are specifically incorporated by reference.

Meganucleases

As disclosed herein editing can be made by way of meganucleases, which are endodeoxyribonucleases characterized by a large recognition site (double-stranded DNA sequences of 12 to 40 base pairs). Exemplary method for using meganucleases can be found in U.S. Pat. Nos. 8,163,514; 8,133,697; 8,021,867; 8,119,361; 8,119,381; 8,124,369; and 8,129,134, which are specifically incorporated by reference.

Delivery

The programmable nucleic acid modifying agents and other modulating agents, or components thereof, or nucleic acid molecules thereof (including, for instance HDR template), or nucleic acid molecules encoding or providing components thereof, may be delivered by a delivery system herein described.

Vector delivery, e.g., plasmid, viral delivery: the modulating agents, can be delivered using any suitable vector, e.g., plasmid or viral vectors, such as adeno associated virus (AAV), lentivirus, adenovirus or other viral vector types, or combinations thereof. In some embodiments, the vector, e.g., plasmid or viral vector is delivered to the tissue of interest by, for example, an intramuscular injection, while other times the delivery is via intravenous, transdermal, intranasal, oral, mucosal, or other delivery methods. Such delivery may be either via a single dose, or multiple doses. One skilled in the art understands that the actual dosage to be delivered herein may vary greatly depending upon a variety of factors, such as the vector choice, the target cell, organism, or tissue, the general condition of the subject to be treated, the degree of transformation/modification sought, the administration route, the administration mode, the type of transformation/modification sought, etc.

Diseases

In certain embodiments, the ex vivo system is derived from a subject with a disease (e.g., to study the disease ex vivo). In certain embodiments, the ex vivo system is used as a cell-based therapy to treat a subject suffering from a disease. The disease may be selected from the group consisting of cancer, autoimmune disease, bone marrow failure, hematological conditions, aplastic anemia, beta-thalassemia, diabetes, motor neuron disease, Parkinson's disease, spinal cord injury, muscular dystrophy, kidney disease, liver disease, multiple sclerosis, congestive heart failure, head trauma, lung disease, psoriasis, liver cirrhosis, vision loss, cystic fibrosis, hepatitis C virus, human immunodeficiency virus, inflammatory bowel disease (IBD), and any disorder associated with tissue degeneration.

Cancer

In certain example embodiments, the pharmaceutical compositions and adoptive cell transfer strategies may be used to treat various forms of cancer. Examples of cancer include but are not limited to carcinoma, lymphoma, blastoma, sarcoma, and leukemia or lymphoid malignancies. More particular examples of such cancers include without limitation: squamous cell cancer (e.g., epithelial squamous cell cancer), lung cancer including small-cell lung cancer, non-small cell lung cancer, adenocarcinoma of the lung, squamous carcinoma of the lung and large cell carcinoma of the lung, cancer of the peritoneum, hepatocellular cancer, gastric or stomach cancer including gastrointestinal cancer, pancreatic cancer, glioma, glioblastoma, cervical cancer, ovarian cancer, liver cancer, bladder cancer, hepatoma, breast cancer, colon cancer, rectal cancer, colorectal cancer, endometrial cancer or uterine carcinoma, salivary gland carcinoma, kidney or renal cancer, prostate cancer, vulval cancer, thyroid cancer, hepatic carcinoma, anal carcinoma, penile carcinoma, as well as CNS cancer, melanoma, head and neck cancer, bone cancer, bone marrow cancer, duodenum cancer, oesophageal cancer, thyroid cancer, or hematological cancer.

Other non-limiting examples of cancers or malignancies include, but are not limited to: Acute Childhood Lymphoblastic Leukemia, Acute Lymphoblastic Leukemia, Acute Lymphocytic Leukemia, Acute Myeloid Leukemia, Adrenocortical Carcinoma, Adult (Primary) Hepatocellular Cancer, Adult (Primary) Liver Cancer, Adult Acute Lymphocytic Leukemia, Adult Acute Myeloid Leukemia, Adult Hodgkin's Disease, Adult Hodgkin's Lymphoma, Adult Lymphocytic Leukemia, Adult Non-Hodgkin's Lymphoma, Adult Primary Liver Cancer, Adult Soft Tissue Sarcoma, AIDS-Related Lymphoma, AIDS-Related Malignancies, Anal Cancer, Astrocytoma, Bile Duct Cancer, Bladder Cancer, Bone Cancer, Brain Stem Glioma, Brain Tumours, Breast Cancer, Cancer of the Renal Pelvis and Urethra, Central Nervous System (Primary) Lymphoma, Central Nervous System Lymphoma, Cerebellar Astrocytoma, Cerebral Astrocytoma, Cervical Cancer, Childhood (Primary) Hepatocellular Cancer, Childhood (Primary) Liver Cancer, Childhood Acute Lymphoblastic Leukemia, Childhood Acute Myeloid Leukemia, Childhood Brain Stem Glioma, Glioblastoma, Childhood Cerebellar Astrocytoma, Childhood Cerebral Astrocytoma, Childhood Extracranial Germ Cell Tumours, Childhood Hodgkin's Disease, Childhood Hodgkin's Lymphoma, Childhood Hypothalamic and Visual Pathway Glioma, Childhood Lymphoblastic Leukemia, Childhood Medulloblastoma, Childhood Non-Hodgkin's Lymphoma, Childhood Pineal and Supratentorial Primitive Neuroectodermal Tumours, Childhood Primary Liver Cancer, Childhood Rhabdomyosarcoma, Childhood Soft Tissue Sarcoma, Childhood Visual Pathway and Hypothalamic Glioma, Chronic Lymphocytic Leukemia, Chronic Myelogenous Leukemia, Colon Cancer, Cutaneous T-Cell Lymphoma, Endocrine Pancreas Islet Cell Carcinoma, Endometrial Cancer, Ependymoma, Epithelial Cancer, Esophageal Cancer, Ewing's Sarcoma and Related Tumours, Exocrine Pancreatic Cancer, Extracranial Germ Cell Tumour, Extragonadal Germ Cell Tumour, Extrahepatic Bile Duct Cancer, Eye Cancer, Female Breast Cancer, Gaucher's Disease, Gallbladder Cancer, Gastric Cancer, Gastrointestinal Carcinoid Tumour, Gastrointestinal Tumours, Germ Cell Tumours, Gestational Trophoblastic Tumour, Hairy Cell Leukemia, Head and Neck Cancer, Hepatocellular Cancer, Hodgkin's Disease, Hodgkin's Lymphoma, Hypergammaglobulinemia, Hypopharyngeal Cancer, Intestinal Cancers, Intraocular Melanoma, Islet Cell Carcinoma, Islet Cell Pancreatic Cancer, Kaposi's Sarcoma, Kidney Cancer, Laryngeal Cancer, Lip and Oral Cavity Cancer, Liver Cancer, Lung Cancer, Lymphoproliferative Disorders, Macroglobulinemia, Male Breast Cancer, Malignant Mesothelioma, Malignant Thymoma, Medulloblastoma, Melanoma, Mesothelioma, Metastatic Occult Primary Squamous Neck Cancer, Metastatic Primary Squamous Neck Cancer, Metastatic Squamous Neck Cancer, Multiple Myeloma, Multiple Myeloma/Plasma Cell Neoplasm, Myelodysplastic Syndrome, Myelogenous Leukemia, Myeloid Leukemia, Myeloproliferative Disorders, Nasal Cavity and Paranasal Sinus Cancer, Nasopharyngeal Cancer, Neuroblastoma, Non-Hodgkin's Lymphoma During Pregnancy, Nonmelanoma Skin Cancer, Non-Small Cell Lung Cancer, Occult Primary Metastatic Squamous Neck Cancer, Oropharyngeal Cancer, Osteo-/Malignant Fibrous Sarcoma, Osteosarcoma/Malignant Fibrous Histiocytoma, Osteosarcoma/Malignant Fibrous Histiocytoma of Bone, Ovarian Epithelial Cancer, Ovarian Germ Cell Tumour, Ovarian Low Malignant Potential Tumour, Pancreatic Cancer, Paraproteinemias, Purpura, Parathyroid Cancer,Penile Cancer, Pheochromocytoma, Pituitary Tumour, Plasma Cell Neoplasm/Multiple Myeloma, Primary Central Nervous System Lymphoma, Primary Liver Cancer, Prostate Cancer, Rectal Cancer, Renal Cell Cancer, Renal Pelvis and Urethra Cancer, Retinoblastoma, Rhabdomyosarcoma, Salivary Gland Cancer, Sarcoidosis Sarcomas, Sezary Syndrome, Skin Cancer, Small Cell Lung Cancer, Small Intestine Cancer, Soft Tissue Sarcoma, Squamous Neck Cancer, Stomach Cancer, Supratentorial Primitive Neuroectodermal and Pineal Tumours, T-Cell Lymphoma, Testicular Cancer, Thymoma, Thyroid Cancer, Transitional Cell Cancer of the Renal Pelvis and Urethra, Transitional Renal Pelvis and Urethra Cancer, Trophoblastic Tumours, Urethra and Renal Pelvis Cell Cancer, Urethral Cancer, Uterine Cancer, Uterine Sarcoma, Vaginal Cancer, Visual Pathway and Hypothalamic Glioma, Vulvar Cancer, Waldenstrom's Macroglobulinemia, or Wilms' Tumour.

Autoimmune Diseases

In certain example embodiments, the pharmaceutical compositions and adoptive cell transfer strategies may be used to treat various autoimmune diseases. As used throughout the present specification, the terms “autoimmune disease” or “autoimmune disorder” used interchangeably refer to a diseases or disorders caused by an immune response against a self-tissue or tissue component (self-antigen) and include a self-antibody response and/or cell-mediated response. The terms encompass organ-specific autoimmune diseases, in which an autoimmune response is directed against a single tissue, as well as non-organ specific autoimmune diseases, in which an autoimmune response is directed against a component present in two or more, several or many organs throughout the body.

Non-limiting examples of autoimmune diseases include but are not limited to acute disseminated encephalomyelitis (ADEM); Addison's disease; ankylosing spondylitis; antiphospholipid antibody syndrome (APS); aplastic anemia; autoimmune gastritis; autoimmune hepatitis; autoimmune thrombocytopenia; Behcet's disease; coeliac disease; dermatomyositis; diabetes mellitus type I; Goodpasture's syndrome; Graves' disease; Guillain-Barre syndrome (GBS); Hashimoto's disease; idiopathic thrombocytopenic purpura; inflammatory bowel disease (IBD) including Crohn's disease and ulcerative colitis; mixed connective tissue disease; multiple sclerosis (MS); myasthenia gravis; opsoclonus myoclonus syndrome (OMS); optic neuritis; Ord's thyroiditis; pemphigus; pernicious anaemia; polyarteritis nodosa; polymyositis; primary biliary cirrhosis; primary myoxedema; psoriasis; rheumatic fever; rheumatoid arthritis; Reiter's syndrome; scleroderma; Sjögren's syndrome; systemic lupus erythematosus; Takayasu's arteritis; temporal arteritis; vitiligo; warm autoimmune hemolytic anemia; or Wegener's granulomatosis.

Other Diseases

In certain embodiments, disease may be treated by infusion of target cell types (see, e.g., US20110091433A1 and Table 2 of application). In certain embodiments, target cell types can be modulated according to the present invention to more faithfully recapitulate the in vivo cells.

Aplastic anemia is a rare but fatal bone marrow disorder, marked by pancytopaenia and hypocellular bone marrow (Young et al. Blood 2006, 108: 2509-2519). The disorder may be caused by an immune-mediated pathophysiology with activated type I cytotoxic T cells expressing Th1 cytokine, especially γ-interferon targeted towards the haematopoietic stem cell compartment, leading to bone marrow failure and hence anhaematoposis (Bacigalupo et al. Hematology 2007, 23-28). The majority of aplastic anaemia patients can be treated with stem cell transplantation obtained from HLA-matched siblings (Locasciulli et al. Haematologica. 2007; 92:11-18.).

Thalassaemia is an inherited autosomal recessive blood disease marked by a reduced synthesis rate of one of the globin chains that make up hemoglobin. Thus, there is an underproduction of normal globin proteins, often due to mutations in regulatory genes, which results in formation of abnormal hemoglobin molecules, causing anemia. Different types of thalassemia include alpha thalassemia, beta thalassemia, and delta thalassemia, which affect production of the alpha globin, beta globin, and delta globin, respectively.

Diabetes is a syndrome resulting in abnormally high blood sugar levels (hyperglycemia). Diabetes refers to a group of diseases that lead to high blood glucose levels due to defects in either insulin secretion or insulin action in the body. Diabetes is typically separated into two types: type 1 diabetes, marked by a diminished production of insulin, or type 2 diabetes, marked by a resistance to the effects of insulin. Both types lead to hyperglycemia, which largely causes the symptoms generally associated with diabetes, e.g., excessive urine production, resulting compensatory thirst and increased fluid intake, blurred vision, unexplained weight loss, lethargy, and changes in energy metabolism.

Motor neuron diseases refer to a group of neurological disorders that affect motor neurons. Such diseases include amyotrophic lateral sclerosis (ALS), primary lateral sclerosis (PLS), and progressive muscular atrophy (PMA). ALS is marked by degeneration of both the upper and lower motor neurons, which ceases messages to the muscles and results in their weakening and eventual atrophy. PLS is a rare motor neuron disease affecting upper motor neurons only, which causes difficulties with balance, weakness and stiffness in legs, spasticity, and speech problems. PMA is a subtype of ALS that affects only the lower motor neurons, which can cause muscular atrophy, fasciculations, and weakness.

Parkinson's disease (PD) is a neurodegenerative disorder marked by the loss of the nigrostriatal pathway, resulting from degeneration of dopaminergic neurons within the substantia nigra. The cause of PD is not known, but is associated with the progressive death of dopaminergic (tyrosine hydroxylase (TH) positive) mesencephalic neurons, inducing motor impairment. Hence, PD is characterized by muscle rigidity, tremor, bradykinesia, and potentially akinesia.

Spinal cord injury is characterized by damage to the spinal cord and, in particular, the nerve fibers, resulting in impairment of part or all muscles or nerves below the injury site. Such damage may occur through trauma to the spine that fractures, dislocates, crushes, or compresses one or more of the vertebrae, or through nontraumatic injuries caused by arthritis, cancer, inflammation, or disk degeneration.

Muscular dystrophy (MD) refers to a set of hereditary muscle diseases that weaken skeletal muscles. MD may be characterized by progressive muscle weakness, defects in muscle proteins, muscle cell apoptosis, and tissue atrophy. There are over 100 diseases which exhibit MD characteristics, although nine diseases in particular—Duchenne, Becker, limb girdle, congenital, facioscapulohumeral, myotonic, oculopharyngeal, distal, and Emery-Dreifuss—are classified as MD.

Kidney disease refers to conditions that damage the kidneys and decrease their ability to function, which includes removal of wastes and excess water from the blood, regulation of electrolytes, blood pressure, acid-base balance, and reabsorption of glucose and amino acids. The two main causes of kidney disease are diabetes and high blood pressure, although other causes include glomerulonephritis, lupus, and malformations and obstructions in the kidney.

Multiple sclerosis is an autoimmune condition in which the immune system attacks the central nervous system, leading to demyelination. MS affects the ability of nerve cells in the brain and spinal cord to communicate with each other, as the body's own immune system attacks and damages the myelin which enwraps the neuron axons. When myelin is lost, the axons can no longer effectively conduct signals. This can lead to various neurological symptoms which usually progresses into physical and cognitive disability.

Congestive heart failure refers to a condition in which the heart cannot pump enough blood to the body's other organs. This condition can result from coronary artery disease, scar tissue on the heart cause by myocardial infarction, high blood pressure, heart valve disease, heart defects, and heart valve infection. Treatment programs typically consist of rest, proper diet, modified daily activities, and drugs such as angiotensin-converting enzyme (ACE) inhibitors, beta blockers, digitalis, diuretics, vasodilators. However, the treatment program will not reverse the damage or condition of the heart.

Hepatitis C is an infectious disease in the liver, caused by hepatitis C virus. Hepatitis C can progress to scarring (fibrosis) and advanced scarring (cirrhosis). Cirrhosis can lead to liver failure and other complications such as liver cancer.

Head trauma refers to an injury of the head that may or may not cause injury to the brain. Common causes of head trauma include traffic accidents, home and occupational accidents, falls, and assaults. Various types of problems may result from head trauma, including skull fracture, lacerations of the scalp, subdural hematoma (bleeding below the dura mater), epidural hematoma (bleeding between the dura mater and the skull), cerebral contusion (brain bruise), concussion (temporary loss of function due to trauma), coma, or even death.

Lung disease is a broad term for diseases of the respiratory system, which includes the lung, pleural cavity, bronchial tubes, trachea, upper respiratory tract, and nerves and muscles for breathing. Examples of lung diseases include obstructive lung diseases, in which the bronchial tubes become narrowed; restrictive or fibrotic lung diseases, in which the lung loses compliance and causes incomplete lung expansion and increased lung stiffness; respiratory tract infections, which can be caused by the common cold or pneumonia; respiratory tumors, such as those caused by cancer; pleural cavity diseases; and pulmonary vascular diseases, which affect pulmonary circulation.

Pharmaceutical Compositions

Target cells of the present invention may be combined with various components to produce compositions of the invention. The compositions may be combined with one or more pharmaceutically acceptable carriers or diluents to produce a pharmaceutical composition (which may be for human or animal use). Suitable carriers and diluents include, but are not limited to, isotonic saline solutions, for example phosphate-buffered saline. The composition of the invention may be administered by direct injection. The composition may be formulated for parenteral, intramuscular, intravenous, subcutaneous, intraocular, oral, transdermal administration, or injection into the spinal fluid.

Compositions comprising target cells may be delivered by injection or implantation. Cells may be delivered in suspension or embedded in a support matrix such as natural and/or synthetic biodegradable matrices. Natural matrices include, but are not limited to, collagen matrices. Synthetic biodegradable matrices include, but are not limited to, polyanhydrides and polylactic acid. These matrices may provide support for fragile cells in vivo.

The compositions may also comprise the target cells of the present invention, and at least one pharmaceutically acceptable excipient, carrier, or vehicle.

Delivery may also be by controlled delivery, i.e., delivered over a period of time which may be from several minutes to several hours or days. Delivery may be systemic (for example by intravenous injection) or directed to a particular site of interest. Cells may be introduced in vivo using liposomal transfer.

Target cells may be administered in doses of from 1×10⁵ to 1×10⁵ cells per kg. For example a 70 kg patient may be administered 1.4×10⁶ cells for reconstitution of tissues. The dosages may be any combination of the target cells listed in this application.

The invention is further described in the following examples, which do not limit the scope of the invention described in the claims.

EXAMPLES Example 1—Benchmarking Paneth Cells of Conventional Organoids with their In Vivo Counterparts

Conventional intestinal organoids produced from the spontaneous differentiation of ISCs have been used to study PCs in vitro in multiple contexts [28,29]. These in vitro PCs exist as part of a heterogeneous system, yet to be rigorously benchmarked against their in vivo counterparts. To better understand the composition of PCs within conventional organoids and how well those PCs approximate their in vivo counterparts, Applicants sought to globally compare the conventional organoid-derived PCs and their in vivo counterpart (FIG. 1A).

To relate the organoid-derived PC state to in vivo PCs, Applicants first generated an unbiased reference in vivo scRNA-seq data set. Applicants performed massively-parallel scRNA-seq using the recently developed Seq-Well platform [31] on epithelial cells from the ileal region of the small intestine acquired as two biological replicates (Methods). Applicants assessed quality metrics for number of genes, unique molecular identifies (UMIs), mitochondrial genes, and ribosomal genes, all of which fell within expectations (all cells average: 1,043 genes, 2,168 UMI, 5.4% ribosomal genes, 10.4% mitochondrial genes). UMI-collapsed cells-by-genes (7,667 cells x 17,505 genes). Expression matrices were analyzed using Seurat (Methods), performing dimensionality reduction, graph-based clustering and deriving lists of cluster-specific genes in order to identify PCs. Within the spectrum of cell types, Applicants identified two clusters (2 and 11) enriched for Lyz1 expression (FIG. 1B,C), of which Applicants determined cluster 11 to be fully mature PCs (n=189 cells) based on uniform expression of a set of associated antimicrobial peptide marker genes such as Defa22, Defa21, and Ang4 (receiver operating characteristic (ROC) test, area under the curve (AUC)>0.99 for markers listed (cluster 11 average: 866 genes, 3,357 UMI, 3.5% ribosomal genes, 4.8% mitochondrial genes) (Table 1). Applicants further utilize these genes (genes with AUC>0.65 for in vivo PC) throughout the study to relate organoid-derived cell states to in vivo PCs. They are fully inclusive of the 14 high confidence markers described for Paneth cells from the terminal ileum in the recently published mouse small intestinal atlas [3]. (NB: Applicants extend the gene list beyond truly specific marker genes that are not expressed in other cell types as Applicants are interested in a more comprehensive set of Paneth-enriched genes for further comparison).

Here, Applicants establish a systematic workflow for characterizing and improving the physiological-representation of to enable the creation of better in vitro models for advancing research and therapeutic development. Taking the PC as a test case, Applicants utilize single-cell transcriptomics to benchmark the current state-of-the-art organoid model against its in vivo counterpart, and identify differences in developmental pathway signaling between in vitro and in vivo cell states. This profiling guides the rational augmentation of pathway activity during stem cell differentiation with a small molecule chemical induction method previously validated to enhance in vitro LYZ1 gene expression in organoids [30]. Applicants validate the pipeline by generating an enhanced in vitro physiological mimic of the in vivo PC, and provide a detailed characterization of the derived cell state through morphologic, proteomic, transcriptomic, and functional assays based on known signatures of in vivo PCs. Furthermore, Applicants use the enhanced model and findings from its transcriptomic and proteomic characterization to identify Nupr1 as a potential stress-response factor that facilitates the survival of PCs, demonstrating the improved ability to examine gene function in vitro within a more representative cell type.

Applicants next performed scRNA-seq using Seq-Well on conventional organoids derived from an ISC-enriched state (FIG. 1A). Beginning with murine small intestinal crypts, Applicants directly enriched for LGR5+ ISCs over six days following isolation within a Matrigel scaffold and medium containing recombinant growth factors EGF (E), Noggin (N), and R-spondin 1 (R), small molecules CHIR99021 (C) and valproic acid (V), as well as Y-27632 for the first two days to inhibit rho kinase and mitigate anoikis, as previously described (ENR+CV) [30]. Cells were passaged into conventional ENR culture for an additional six days to allow multi-lineage differentiation and produce stem cell-derived in vitro PCs. Following scRNA-seq, Applicants computationally identified six clusters (amongst 2,513 cells x 16,198 genes meeting quality standards, see Methods) in ENR organoids, which Applicants label as ENR1-4, and EEC-1 and -2, for two enteroendocrine cell types (FIG. 1D). Applicants identified ENR-4 as the cluster most enriched for Lyz1 and the PC reference gene set (effect size 0.721, ENR-4 vs all ENR, *t-test p<2.2×10⁻¹⁶) (FIG. 1E,F). Having identified ENR-4 as the cell state of interest in organoids, Applicants directly compared the top 200 most Paneth-like cells in ENR-4 to in vivo PCs by performing differential expression analysis (FIG. 1G). In comparing the two cell types, it became evident that the majority of genes enriched by in vivo PCs were defensins and antimicrobials, including Defa22, Defa21, Zg16, Ang4, Defa3, and Lyz1 (all p<2.92×10⁻³⁷, bimodal test, Bonferroni corrected for multiple comparisons) (FIG. 1G,H). ENR-4 cells were enriched for Chgb, an enteroendocrine marker, and translational biosynthetic genes likely indicative of the high rates of proliferation present in ENR organoids (FIG. 1G). Beyond these selected genes, Applicants note a global reduction in the fraction of the transcriptome of ENR-4 cells producing the total cadre of in vivo PC marker genes (effect size 1.25, InVivo vs. ENR, *t-test p<2.2×10⁻¹⁶), suggesting that the current in vitro organoid-derived PCs are suboptimal for physiological studies (FIG. 1I).

Modulating key developmental pathways of stem cell-derived systems has emerged as a paradigm in bioengineering to rationally generate cell types for basic research and therapeutic aims [32,33]. Specifically, modulating Wnt and Notch signaling has been suggested in the literature to increase the frequency and magnitude of Lyz1 expression and protein in ISC-derived cells [30,34-36]. Leveraging the single-cell transcriptomes of the in vitro and in vivo-derived PCs, Applicants confirmed that Wnt-target genes are enriched in vivo relative to in vitro PCs (effect size 0.559, InVivo vs. ENR, *t-test p<2.035×10⁻⁸) and Notch-target genes were decreased (effect size −0.500, InVivo vs. ENR, *t-test p<5.25×10⁻⁷) (FIG. 1I, Table 2). As a result, Applicants sought to comprehensively test if driving Wnt and inhibiting Notch truly results in a more physiologically representative PC versus the organoid-derived PC, beyond increased expression of Lyz1.

Example 2—Chemical Induction of Wnt and Inhibition of Notch Drives Paneth-Cell Marker Enrichment

Beginning with an LGR5+ ISC-enriched population (ENR+CV), Applicants sought to profile how the modulation of Wnt and Notch signaling through small molecule inhibitors would alter the in vitro PC state, as suggested by the transcriptional profiling. Applicants performed chemical induction (CI) using the previously identified compounds C to drive Wnt signaling and DAPT (D), a gamma-secretase inhibitor, to inhibit Notch (ENR+CD) (FIG. 2A) and measured gene expression of ISC (Lgr5) and PC (Lyz1, DefA1, Mmp7) markers every two days for six days total (FIG. 2B). ENR+CD-treated cells had statistically significant increases in Lyz1 (adj. p=0.005, see Methods) and Mmp7 (adj. p=0.005) within two days compared to ENR, with differences plateauing around four days. DefA1 (adj. p=0.004) expression was significantly increased by day four and plateaued by day six in ENR+CD versus ENR populations. Lgr5 expression in ENR+CD at two days versus ENR showed an insignificant plateau of expression, which trended down by six days. This may be indicative of an expansion in ‘label-retaining’ secretory precursors [37]. Precursor population ENR+CV had no significant difference in PC or ISC markers relative to ENR. The significant increase in PC gene expression in ENR+CD relative to ENR and ENR+CV over the six-day treatment suggests rapid enrichment following CI, supporting the hypothesis that alterations in Wnt and Notch result in superior PC enrichment in vitro.

To phenotypically describe PC enrichment following CI, Applicants performed imaging and immunocytochemistry for PC-associated features. After six days of ENR+CD, cell populations exhibited darkened annular morphology consistent with increased numbers of granule-rich cells (FIG. 8A). Confocal microscopy of whole cell clusters stained for anti-DEFA and anti-LYZ showed an increase in LYZ+ and DEFA+ cells in ENR+CD compared to both ENR and ENR+CV (FIG. 2C). Single-cell counting of confocal imaging showed a significant increase of DEFA and LYZ co-staining cells in ENR+CD (20-30% of cells) versus either ENR or ENR+CV (both <5%) (adj. p=0.0001) (FIG. 8B). Additionally, normalized z-axis profiles of individual co-staining cells within cell clusters revealed a consistent distribution of DEFA (luminally-polarized) and LYZ (diffuse) (FIG. 8C 1-3). High-resolution fluorescent imaging of individual co-staining cells from freshly-isolated small intestinal crypts (in vivo equivalent) and six day-ENR+CD-treated cells showed similar polarized distribution of LYZ and DEFA-staining granules, although freshly-isolated cells appeared to be more granular than CI-PCs (FIG. 2D).

To confirm the extent of enrichment seen in whole population imaging, the prevalence of PCs in ENR+CD relative to ENR was assessed by flow cytometry over the course of 12 days. Applicants identified an in vivo PC phenotype as CD24 and LYZ co-positive cells, per previous reports [38], and noted the presence of single-positive LYZ+ or single-positive CD24+ populations, indicative of alternative cell differentiation, immature, or non-physiological PCs. ENR+CD had substantial enrichment at all time points for double-positive, and single-positive LYZ+ or CD24+ populations relative to ENR, as well as a consistent decrease in double negative population consistent with the PC phenotype (FIG. 2E) (representative populations FIG. 8D, representative gating FIG. 8E). Notably, both ENR and ENR+CD experience declines in total cell viability, with ENR+CD having greater survival at longer times, suggesting both a reduction in anoikis, a potentially physiological ‘long-lived’ PC phenotype in ENR+CD versus ENR, or an enhancement in niche-supporting functionality (FIG. 8F). Overall, imaging and flow cytometry demonstrate a significant increase in cells morphologically resembling in vivo PCs with respect to granularity, polarity, and antimicrobial co-expression in ENR+CD compared to conventional ENR organoids (FIG. 2C-E & 8A-F).

Example 3—Chemically-Induced Paneth Cell Proteome is Enriched for Components of Secretory Lineages

With ENR+CD apparently providing a more prevalent and physiological PC population, Applicants sought to more globally characterize the differences between in vitro PCs (ENR vs. ENR+CD at six days). Because PCs are highly secretory, protein-rich cells, Applicants sought to assess the total intracellular proteome between conditions through liquid chromatography mass spectrometry (LC-MS/MS)-based proteomics. Applicants quantified relative protein abundance across eight samples using isobaric mass tag labeling from four ENR and four ENR+CD samples (M1-1 through M2-2, first digit denotes biological donor, second digit denotes technical replicate) (FIG. 3A). Samples were processed and analyzed in a single 10-plex by LC-MS/MS (FIG. 9A). Applicants identified 8,015 unique proteins within all samples; each replicate pair (ENR+CD/ENR) was normally distributed (FIG. 9B) and correlated with all others, indicating consistent proteome enrichment (FIG. 9C). Approximately 21% of the ENR+CD-enriched proteins (+2σ fold change) were present in all four samples, while 38% were unique to specific samples (FIG. 9D). In contrast, only 7% of the ENR-enriched proteins (−2σ fold change) were present in all four samples, while 51% of the proteins were unique, suggestive of greater heterogeneity in conventional organoids (ENR) as compared to ENR+CD (FIG. 9E). In total, the intracellular proteome of ENR+CD shows relatively consistent protein set enrichment across samples.

Applicants next looked at the sample pairs in aggregate and classified proteins significantly enriched in ENR+CD and ENR by a false discovery rate (FDR)<0.05 and log fold change (±2σ) (FIG. 3B and Table 3). There were 249 ENR+CD-enriched proteins, 212 ENR-enriched proteins, and 7,553 shared proteins. Known PC markers, including LYZ, DEFAs, and other secretory pathway components, were identified as significantly enriched in ENR+CD versus ENR alone. Of known antimicrobial proteins produced by PCs, Applicants detected 10 DEFAs, 5 CRS peptides, 6 ribonucleases, 12 lectins, LYZ1, and PLA2G1B with differential abundance between ENR+CD and ENR (FIG. 3C). Each class of antimicrobials had at least one ENR+CD enriched protein (+2σ), with the ribonucleases significantly enriched and a majority of the lectins and DEFAs unregulated between the two conditions. Proteins associated with the EEC lineage (secretogranins, chromogranins, and neuropeptides) were also enriched in ENR+CD, in addition to multiple other secreted components, including Wnt ligands, and the complement pathway components C3 and CFI. To affirm the reproducibility of the associated proteins in the ENR+CD-enriched proteome, Applicants performed relative quantification within differentiation sets. The coefficient of variation (CoV) of the 249 ENR+CD-enriched proteins within the four ENR+CD samples lies within the expected variation of the detection method, as does the CoV for the 212 ENR-enriched proteins observed across the four ENR samples (FIG. 3D). Low variation across samples in both condition-enriched sets suggests the PC and EEC enrichment occur together, as opposed to distinct samples preferring a lineage during CI. In sum, Applicants see a broad diversity of PC-associated antimicrobials with some enrichment of EEC-associated proteins in ENR+CD relative to ENR.

Example 4—Proteome Enrichment Analysis Reveals Expected Components of Paneth and Secretory Cells and Potential Nuclear Receptor Regulation of Differentiation

To further describe cell lineage of the CI-PC proteome, Gene Set Enrichment Analysis (GSEA) [39,40] was performed. Using an alternative de facto in vivo PC gene set [16] (top 500 genes PC vs. ISC microarray) on the full rank-ordered proteome (ENR+CD/ENR), GSEA provided a normalized enrichment score (NES) of 3.11, FDR q-value <0.0001, and 58% of tags coming before the leading edge, indicating that the CI-PC culture was enriched for the proteins of previously identified PC genes identified in bulk transcriptomic measurements (FIG. 3E). Applicants also identified transcription factors (TFs) that may mediate PC-specific differentiation using GSEA with the MSigDB transcription factor target (v5.2) gene set database [41] with a moderately conservative cutoff (see Methods). Applicants generated an enrichment map [42,43] of several TF targets significantly enriched in both the ENR+CD and ENR proteomes. In ENR+CD, the nuclear receptors for progesterone (PR), aldosterone (AR), and glucocorticoid (GR), as well as the cellular differentiation-implicated TAL1, RP58, and NRSF, are significantly enriched. In ENR, the primary known enrichment was for the cell cycle and proliferation-related E2F TF family (FIG. 3F). These potential TFs are consistent with CI-PC treatment driving expected terminal differentiation of specialized cells, as opposed to conventional organoid culture, which supports a broad mix of intestinal epithelial cells, including proliferating populations. Furthermore, this analysis suggests potential targets, such as PR, AR, and GR, to modulate the differentiation programs of this secretory cell population in future studies.

Finally, Applicants characterized enriched biological functions (BP), cellular compartments (CC), and molecular functions (MF) using DAVID v6.8 and the gene ontology database (GO). All sets had high database coverage (greater than 85%) of queried proteins. The ENR+CD proteome is significantly enriched for extracellular and protein processing compartments and secretory-associated functions (FIG. 10A), while the ENR proteome favors translation, intracellular compartments, and translational activities (FIG. 10B). Of note are the extracellular exosome and calcium ion-binding associated proteins in the ENR+CD proteome that are indicative of the intestinal epithelial secretory phenotype (for complete list of DAVID enrichments, refer to Table 4). These functional enrichments further support that the ENR+CD-cultured organoids are enriched in secretory cells, including PCs, although it does not rule out potential co-enrichment for the EEC lineage.

Example 5—Single-Cell RNA Sequencing Reveals Subsets in Chemically-Induced Paneth Cells that Show Improved Transcriptional Similarity with In Vivo Paneth Cells

With the apparent co-enrichment of canonical PC and EEC proteins in the ENR+CD proteome, Applicants sought to identify whether Applicants produce a homogenous population of mixed-lineage secretory cells or a spectrum of unique cell states between EEC and PC. Applicants performed scRNA-seq using the Seq-Well platform on cells from ENR+CD and the precursor ENR+CV conditions to analyze alongside conventional ENR organoids. To ensure experimental robustness, Applicants assessed quality metrics for number of genes, unique molecular identifiers (UMIs), mitochondrial genes, and ribosomal genes by cluster, all of which fell within expectation (FIG. 11). UMI-collapsed digital gene expression matrices were analyzed using Seurat (Methods); and displaying all three treatments (ENR+CV, ENR, ENR+CD) in tSNE space demonstrated clear separation between each condition (FIG. 4A). This illustrates unique transcriptional differences induced by each treatment conserved across all cells. Plotting key genes demonstrated that, as expected, all cells expressed high levels of Epcam; ENR+CV cells had enhanced Mki67, a marker of proliferation; the ENR+CD condition enriched for cells expressing antimicrobial Lyz1, Defa24, Defa3, Mmp7, and EEC marker Chga; and ENR enriched for absorptive marker Fabp2-expressing cells (FIG. 4B).

To assess sub-population structure and provide a more robust measure of composition beyond canonical marker genes, Applicants performed unsupervised KNN graph-based clustering on the captured cells (FIG. 4C,D and Table 1 for full gene lists), distinguishing four clusters in each treatment condition. Applicants then scored individual clusters according to the amount of the transcriptome within each cell dedicated to synthesizing the respective enriched proteins from the bulk proteome data. Applicants observed that ENR+CD clusters yield a significant enrichment for those proteins detected in the up-regulated proteome (effect size 1.38 ENR+CD vs ENR clusters, p<2.2×10⁻¹⁶) and that the down-regulated proteins were enriched in the ENR and ENR+CV conditions (FIG. 4D,E and data not shown). Intriguingly, at the level of clusters, the upregulated proteome was not evenly distributed across all cells in ENR+CD, but rather most enriched in cluster ENR+CD-4 (effect size 2.40 ENR+CD-4 vs all cells, p<2.2×10⁻¹⁶) (FIG. 4D,E).

To address ENR+CD composition and how it relates to conventional organoids, Applicants interrogated the expression of Lyz1, Chga, and other select genes across each cluster (FIG. 5A). Applicants noted that clusters ENR-4 and ENR+CD-4 shared expression of Lyz1, Defa24, Defa3, and Mmp7, yet ENR+CD-4 cells produced significantly more of each canonical PC gene (bimodal test, p<6.80×10⁻⁷⁴ for genes listed, Bonferroni corrected for multiple comparisons). Furthermore, both ENR-4 and ENR+CD-4 cells lacked expression of EEC genes like Chga, which was observed in the EEC-1 and EEC-2 clusters arising from mixed-grouping of the sample, as well as in ENR+CD-2 and ENR+CD-3 (FIG. 5A). Altogether, this suggests that ENR+CD drives PC differentiation while also inducing a secretory transition state (ENR+CD-2 and 3) expressing a mix of PC and EEC marker genes (Table S1 for full gene lists).

Applicants next sought to compare the states generated in vitro to those observed in vivo with the refined system. Using the gene list of in vivo PC markers and further defining a list for in vivo EECs (see Methods) captured on the Seq-Well platform (Table 1), Applicants observed that the percentage of a cell's transcriptome dedicated to synthesizing defining Paneth genes was significantly enriched relative to ENR-4 in clusters ENR+CD-2, 3 and 4 (effect size 0.15, p<3.43×10⁻⁵; effect size 0.829, p<2.2×10⁻¹⁶; effect size 2.52, p<2.2×10⁻¹⁶, respectively) with an increase in expression of EEC genes across ENR+CD-1, 2 and 3 but not ENR+CD-4 (effect size 1.30, p<2.2×10-16; effect size 1.82, p<2.2×10-16; effect size 1.118, p<2.2×10⁻¹⁶; effect size 0.0465, p=0.2339, respectively) (FIG. 5B). Notably, ENR+CD4 cells (˜10%) had a three-fold increase in the transcriptional resemblance to in vivo PCs relative to ENR-4 (53.4% of transcriptome ENR+CD-4 vs. 16.5% of transcriptome ENR-4) (quantification of FIG. 5B). Furthermore, 45% of ENR+CD cells express a secretory Paneth-like transcriptional phenotype that is at least two-fold enhanced relative to conventional organoids (33.9% of transcriptome ENR+CD-3 and 4 vs. 16.5% ENR-4). Comparing the ENR+CD4 cells relative to in vivo PCs demonstrated striking similarity relative to the difference observed between in vivo and ENR-4 cells (Paneth cell fraction of in vivo transcriptome: effect size 0.237 InVivo vs. ENR+CD-4, p<0.0055; effect size 1.25 InVivo vs ENR-4, p<2.2×10⁻¹⁶, Table 1).

In FIG. 5C, Applicants present a heatmap of scaled expression values for the top genes (AUC>0.65) used for the in vivo Paneth score across ENR-4, ENR+CD-4, and the in vivo cluster used to define PCs. Applicants observe that the enhanced PC phenotype in ENR+CD-4 (effect size 1.144 ENR+CD4 vs ENR-4, p<2.2×10⁻¹⁶) correlates with greater expression of signature genes, such as Lyz1, Lyz2, and Defa5, and greater diversity of antimicrobial peptides genes, such as Ang4, Defa3, and the metalloprotease Mmp7.

To confirm and extend the findings of pathway-based modulation, Applicants scored clusters for enrichment or depletion of canonical growth factor-induced pathways. CHIR activates the Wnt pathway, and Applicants observed a significant enrichment for Wnt target genes in all CI-PC clusters (effect size >0.999, p<2.2×10⁻¹⁶ for all ENR+CD clusters vs ENR-4) (FIG. 12A). While DAPT is a Notch pathway inhibitor, levels of Notch target genes were largely greater than or equivalent to ENR-4 cells across CI-PC clusters, except for significant depletion in ENR+CD-4 (effect size −0.658, p<2.2×10⁻¹⁶ ENR+CD-4 vs ENR-4) (FIG. 12B). This suggests that complete Notch suppression is key for PC differentiation distinct from an EEC fate. As well, given the recognized role for distinct respiratory potential in enterocytes, ISCs, and PCs, Applicants scored cells across respiratory electron transport genes [44,45]. ENR+CD-4 had the lowest cluster score relative to all cell subsets (effect size −1.4649, p<2.2×10-16) (FIG. 12C). Together, this suggests that Wnt signaling is necessary but not sufficient to specify the mature PC phenotype and that Notch and metabolic conditions play a larger role in the decision between PC and EEC fates.

Example 6—Chemically-Induced Paneth Cells Mimic In Vivo Stimulant-Induced Secretion and Demonstrate Selective Modulation of Bacteria in Co-Culture

In addition to the morphological, proteomic, and transcriptional characterization of PC phenotype in ENR+CD and ENR, Applicants sought to measure physiological function by assessing stimulant-induced secretion of antimicrobials. Applicants assessed the dynamics of LYZ accumulation in media supernatant of cultures following media wash, basally and after stimulation with carbachol (CCh), a cholinergic agonist known to induce PC secretion [46]. 10 μM CCh induced a rapid accumulation of LYZ within two hours that plateaued around six hours post-wash (2-way ANOVA, stimulant p<0.0001, time-point p<0.0001) (FIG. 6B). The observed PC secretion in response to CCh is consistent with observations made in ex vivo crypts, though over appreciably longer time scales, likely due to the added diffusion barrier of the organoid structure and matrigel [46]. Applicants next identified how LYZ secretion changes over the course of differentiation. Beginning with an ISC-enriched population, Applicants assayed for secreted LYZ in cell culture supernatants every two days for six days of ENR+CD culture, following a 24-hour stimulation with CCh or without (basal collection/non-stimulated). Notable increases in functional secretion (stimulated relative to basal) occurred at days four and six (2-way ANOVA, stimulant p<0.0001, time-point p<0.0001) (FIG. 6A). Compared to conventional organoids and ISC-enriched precursors, ENR+CD secreted significantly more basal LYZ (p<0.0001) and was the only population that showed grossly measurable CCh-induced secretion (adj. p=0.03) (FIG. 6C). This result is consistent with the observed enrichment, and demonstrates a system to easily measure physiologic PC antimicrobial secretion.

Based on the broad spectrum of antimicrobials detected proteomically, transcriptionally, and functionally, Applicants hypothesized that ENR+CD possess greater bactericidal effects than conventional organoids. Applicants assayed for bacterial growth modulation by suspending cell clusters with common laboratory strains of gram-negative and gram-positive bacteria in exponential growth. CI-PCs significantly suppressed growth of gram-positive L. lactis MG1363 (adj. p=0.0001), which did not occur with conventional organoids, indicative of increased PC-associated antimicrobial activity. Both ENR (adj. p=0.0005) and ENR+CD (adj. p=0.01) co-culture showed significant increase in gram-negative E. coli MG1655 growth but no appreciable effect on the growth of gram-positive E. faecalis V583 versus bacteria alone (FIG. 6D). While this assay simplifies the PCs' physiological environment and may not be a direct proxy for strain-specific growth modulation, it does demonstrate that the PC-enrichment of ENR+CD versus conventional organoids enables detectable in vitro bacteria species-specific PC antimicrobial response, opening avenues for future experimentation.

Example 7—Chemically-Induced Paneth Cells Provide Niche Support and Enhance Conventional Organoid Survival

Beyond the generation of antimicrobial peptides, PCs provide niche support for ISCs. Applicants sought to test if CI-PCs provided niche factors known to drive epithelial regenerative turnover. Applicants performed co-culture experiments, mixing and re-plating cell populations derived from six-days of ENR or ENR+CD culture and assayed co-culture viability, caspase activity, and cytotoxicity 24 and 48 hours following re-plating in ENR-media. If there were no appreciable interaction, positive or negative, between the two populations Applicants would expect to see a linear trend of every measured variable throughout mixing ratios. However, Applicants observe a significant positive interaction where the presence of both populations drives an overall increase in cellular viability, beginning at 24 hours (one sample t-test 1:1 p=0.037) and increasing at 48 hours (one sample t-test 1:1 p=0.001 and 1:3 p<0.001) (FIG. 6E). This is likely due to a significant decrease in overall apoptosis relative to the total cell population (one sample t-test 24-hour 1:1 p=0.004 and 1:3 p=0.032, 48-hour 1:3 p=0.003), and unrelated to changes in cellular cytotoxicity. Applicants believe that the presence of a PC-enriched population (from ENR+CD) is driving this effect by providing increased soluble regenerative factors to the ISC population in ENR organoids, increasing the generation of new cells, and resulting in a lower overall rate of apoptosis.

Example 8—Mapping of In Vivo Paneth Cell-Associated Transcription Factors to In Vitro Proteome and Transcriptome Reveals Nupr1 as Important in Epithelial Survival

Lastly, Applicants sought to use this physiologically-improved in vitro PC system (ENR+CD) to identify novel factors potentially supportive of PC survival or differentiation. Using the in vivo PC and EEC gene lists, and filtering for only transcription factors (TFs) (using TFdb, downloaded September 2017) [47], Applicants identified a set of PC- or EEC-specific TFs. Applicants mapped these TFs to the in vitro proteome (FIG. 7A & Table 3), which revealed the previously-unreported NUPR1 as the most enriched PC-specific TF in ENR+CD. This finding was supported by differential expression between ENR+CD2 (most enteroendocrine-like cells) and ENR+CD4 (p<3.12×10⁻³⁷, bimodal test, Bonferroni corrected for multiple comparisons) (FIG. 7B). Applicants further identified Nupr1 in the in vivo PC populations which showed specific and enriched expression of Nupr1 by in vivo PCs (ROC test, AUC=0.833) (FIG. 7B). Intriguingly, Nupr1 is a stress-response gene, known to promote cellular survival and senescence through mediation of autophagy, and has primarily been studied in the context of cancer [48-50]. Autophagy and stress response have repeatedly been implicated through GWAS study in PCs in IBD, however Nupr1 has only ever been reported in a single IBD GWAS study, and its role in PC biology has not been formally investigated [51]. With the model, Applicants sought to test the role of NUPR1 on in vitro PC survival, through the small molecule inhibition of NUPR1 with trifluoperazine (TFP) [52,53]. Applicants first tested how different dosages impact PC differentiation in combination with ENR+CD for six days, where doses above luM lead to near total cell death, and where the few surviving cells are primarily non-Paneth (FIG. 7C). This suggests that Nupr1 is likely critical to cellular survival during the CI-differentiation process. Applicants also tested the addition of TFP for two days following a six-day course of ENR+CD, where again Applicants see a profound, but not total, decline in cellular viability. Further, it appears that TFP treatment is selectively more toxic to PC and PC-progenitor populations relative to non-PC populations (FIG. 7D). In total, this initial investigation suggests that NUPR1 may be a critical TF in PC development and survival, which carries therapeutic implications and Applicants will seek to validate in vivo in future work.

Example 9—Discussion

Applicants sought to directly compare a specific cell type present in vivo to that derived in vitro, with the main goal of understanding the nature and extent of divergence between the in vivo and in vitro conditions. Empowered by recent advances in massively-parallel scRNA-seq, Applicants define the current cell types and propose a potentially improved cell state derived through rational modulation of developmental pathways. Applicants identified that the PC-state of conventional intestinal organoid shows a poor representation of antimicrobials, and that modulation of Wnt and Notch during differentiation may improve physiological representation. To this end, Applicants enriched and expanded primary murine adult LGR5+ ISCs, which are stable over many divisions [54], to provide a near-unlimited pool from which to differentiate starting from minimal adult tissue. This “ground state” expansion prior to differentiation is an emerging theme within models to characterize epithelial biology in vitro [9,10,55,56].

Using targeted small molecule promotion of Wnt and inhibition of Notch signaling, Applicants drove a secretory differentiation program and enriched for mature PCs with greater diversity and expression of antimicrobial peptides relative to existing in vitro models and, thus, are more representative of in vivo PCs. Imaging of this population revealed that they are positive for the antimicrobials LYZ and DEFA, clearly polarized, and granule-rich, suggestive of a mature PC. This population is approximately six-fold more abundant in ENR+CD than an ENR organoid, as confirmed through image quantification, flow cytometry and scRNA-seq. Applicants further characterized the subpopulation enrichments of the ENR+CD culture and directly compared it to conventional organoids. Applicants identified two subpopulations in scRNA-seq (ENR+CD-3 and ENR+CD-4) that account for approximately half of the ENR+CD-treated cells with a high-degree of transcriptional similarity to in vivo PCs, a greater percentage/matching than the ENR-subpopulation that most resembles an in vivo PC (ENR-4). From this analysis, Applicants believe that in vitro PCs characterized in the past [28,29] likely represent secretory precursor populations lacking the full phenotypic repertoire of the in vivo PC, which Applicants identify as the approximately 5% of single-staining LYZ+ cells present in ENR organoids as assessed by flow cytometry (FIG. 2E). The in vitro PCs, however, are morphologically, transcriptionally, and functionally representative of their in vivo counterparts, easily generated from primary tissue samples, and can provide near unlimited numbers of PCs for further studies. While this approach moves us much closer to generating the in vivo cell type (Paneth cell fraction of in vivo transcriptome: effect size 0.237 InVivo vs. ENR+CD-4, p<0.0055; effect size 1.25 InVivo vs ENR, p<2.2×10⁻¹⁶), Applicants still do not capture the total amount of antimicrobial peptides present in vivo, and propose pathways to modulate in future studies.

Evidence suggests that PC antimicrobial expression and function are influenced by genetic background [57] and implicated in intestinal disease, including IBD [58]. The identical genetic background of the population Applicants studied likely influenced the observed low variation in protein abundance within the ENR+CD-enriched proteome. How genetic background may influence differentiation through this protocol is yet to be studied but especially prudent, as Applicants demonstrated the ability to detect a broad spectrum of antimicrobial proteins and peptides and their differential abundance within a PC-enriched population. Interestingly, Applicants identified that the same sub-population (ENR+CD-4) with the most transcriptional overlap to the bulk ENR+CD-enriched proteome also most closely resembles the in vivo PC. While this sub-population does not account for the majority of ENR+CD-cultured cells, it appears that ENR+CD-4 consistently drives the PC phenotype in vitro. In addition to assessing the role of genetic background or disease state on antimicrobial content, the platform also affords the ability to interrogate how alterations in protein processing and storage in PCs affects the proteome, which has been shown to drive shifts in the microbiome and may be implicated in disease [59,60]. Finally, while Applicants demonstrate an enriched phenotypic spectrum of antimicrobials and Wnt ligands, Applicants also identified several neuropeptides and hormone products associated with the EEC lineage within the system. Given that multiple studies have linked the differentiation of PCs and EECs through a common progenitor population [61], it is reasonable to expect enrichment in one population would also allow for some overlap with the other, as Applicants see in the scRNA-seq.

To understand how the chemical induction led to distinct secretory sub-populations within the CI-PCs, Applicants mapped Wnt, Notch, and metabolic gene sets onto each subpopulation. In the system, Notch-signature is highest in the stem cells and EECs, lower in enterocytes, and lowest in PCs. The system's Wnt signature is relatively decreased in enterocytes (ENR largely) and increased in PCs and EECs, which both occur predominantly in the Wnt-driven condition ENR+CD (CI-PCs). In total, this suggests that Wnt is necessary for ISCs to commit to PC and EEC lineages and that future experimentation with specific synthetic Wnt ligands [62] may prove fruitful in distinguishing Wnt target genes that discriminatorily yield PCs or EECs. Also clear is that strong Notch inhibition is important for mature PC development, possibly as a balance between differentiation and cell survival. Future studies should incorporate temporal aspects to growth factor delivery akin to what has been shown for degradable matrices [63] to enhance purity and yield. Finally, Applicants see a notable gradient in cellular respiration across subpopulations, lowest in the PC and highest in the stem cell and EEC lineages, in agreement with recent work on the metabolic differences within the stem cell niche [45], as another potential cue to further specify PC differentiation. In all, the analysis of single cell heterogeneity shows that the system is well-positioned to further investigate the effects of both known and unknown physiological cues on PC differentiation and function.

One of the most important features Applicants established with the CI-PCs was the ability to measure PC functional enrichment through simple soluble assays. Applicants demonstrated sufficient functional enrichment in PCs such that enzymatic activity assays can detect stimulant-induced secretion of antimicrobials as well as the promotion of the ISC niche. Moreover, microbe co-culture assays with the enriched cells produce measurable and selective microbial growth modulation not observed using conventional organoids. Co-culture strains were chosen to demonstrate proof of concept of selective antimicrobial action and assess functionality compared to conventional organoids. Given the results showing selective modulation of bacterial growth, Applicants believe that the system could serve as a tool to further probe host-microbe interaction in vitro. Furthermore, it would allow for investigations of both microbial mechanisms that elicit PC response (e.g. TLRs) and the properties of complex mixtures of secreted components, including multiple antimicrobial proteins.

The generation of comprehensive cellular atlases from humans and model organisms will certainly yield a revolution in the understanding of complex tissues [3]. Intestinal organoids have already proven their value in studying human and murine epithelial biology. However, to rigorously test hypotheses of basic biological or disease mechanism, it will be essential to have reliable protocols for the generation of specialized subsets of cells which cannot be readily isolated from tissue. The representativeness of cell states present in organoids and the specialized cell types present in vivo [3] is an outstanding question with implications in mucosal immunology, developmental biology, and translational medicine. The single-cell genomics approach provides compelling evidence that organoid-derived cell populations must be validated to ensure physiological relevance, and additionally provides a rational framework for identifying cell states and their potential upstream drivers to modulate cellular composition. This approach could enable advances beyond conventional organoid systems to provide an enriched highly-specialized cell population that recapitulates important physiological functions of the intestinal epithelium, and could represent an improvement in in vitro PC culture for the purposes of high-throughput screening, the study of host-microbe interactions, bioengineering (e.g. precision gene editing), and the identification of novel genetic candidates in PC function (e.g. Nupr1). With this framework, Applicants illustrate the power and importance of rigorously characterizing the specialized cell types derived in organoids to those defined in “atlas-level” surveys of the intestinal epithelium.

Example 10—Methods

Mice for Tissue Isolation.

Proximal small intestine was isolated from C57BL/6 mice of both sexes, aged between three to six months in all experiments.

Bacteria Strains.

Cells were stored at −80C and grown as follows. E. coli strain MG1655 was grown overnight in LB. For experiments, overnight cultures of MG1655 were resuspended in M9 supplemented with 0.4% glucose and 0.2% cas amino acids. L. lactis strain MG1363 was grown in M17 media supplemented with 0.5% glucose, and E. faecalis strain V583 was grown in Brain Heart Infusion (BHI) media.

Crypt Culture, Enrichment, and Differentiation.

Small intestinal crypts were cultured as previously described [64]. Briefly, crypts were resuspended in basal culture medium (Advanced DMEM/F12 with 2 mM GlutaMAX and 10 mM HEPES; Thermo Fisher Scientific) at a 1:1 ratio with Corning™ Matrigel™ Membrane Matrix—GFR (Fisher Scientific) and plated at the center of each well of 24-well plates. Following Matrigel polymerization, 500 μL of small intestinal crypt culture medium (basal media plus 100× N2 supplement, 50× B27 supplement; Life Technologies, 500× N-acetyl-L-cysteine; Sigma-Aldrich) supplemented with growth factors EGF-E (50 ng/mL, Life Technologies), Noggin—N (100 ng/mL, PeproTech) and R-spondin 1—R (500 ng/mL, PeproTech) and small molecules CHIR99021—C (3 μM, LC Laboratories) and valproic acid—V (1 mM, Sigma-Aldrich) was added to each well. ROCK inhibitor Y-27632—Y (10 μM, R&D Systems) was added for the first 2 days of culture. Cells were cultured at 37° C. with 5% CO₂, and cell culture medium was changed every other day. After 6 days of culture, crypt organoids were isolated from Matrigel by mechanical dissociation. Isolated organoids were resuspended in TrypLE Express (Life Tech) to dissociate into single cells, then replated in Matrigel with ENR+CV+Y media for 2 days. Cells were once again passaged, either into freezing media (Life Tech) for cryopreservation or replated at approximately 200 organoids per well (24-well plate) for ISC-enriched organoid expansion. ISC-enriched organoids were passaged or differentiated every 6 days in the ENR+CV condition. To differentiate, cells were passaged as previously described, and crypt culture medium containing growth factors ENR only or ENR+CD (D—DAPT, 10 μM; Sigma-Aldrich) was added to each well.

RNA Extraction & qRT-PCR.

Organoids were isolated from Matrigel in 24-well plates following culture as previously described, and pellets were lysed in TRI reagent with RNA extracted according to the manufacturer's protocol (T9424, Sigma). Resulting RNA pellets were dissolved in UltraPure water and cDNA synthesis was performed using QuantiTect Reverse Transcription Kit (Qiagen). qPCR reactions were performed using TaqMan Universal Master Mix II (no UNG), pre-designed TaqMan probes (Table S5), and 500 ng of sample cDNA (LifeTech). Reactions were carried out using an Applied Biosystems 7900HT system. qPCR results were analyzed using RQ manager 1.2 software to obtain CT values used for relative quantification to the housekeeping gene Hprt.

Confocal Imaging of Whole Cell Clusters.

ISC-enriched cell clusters (ENR+CV) suspended in 40 μL of Matrigel were seeded onto round coverslips inside a 24-well plate. Cells were treated with ENR+CD, ENR+CV, or ENR as previously described. At day 6, organoids were rinsed (PBS0 3×) and fixed to the coverslips by incubating with 4% paraformaldehyde (PFA) for 30 minutes at room temperature (RT). Gels were blocked and permeabilized by incubating at RT for one hour with 0.1% Triton X-100 and 5% Powerblock in PBSO. Organoids were stained for DEFA and LYZ by incubating with rat anti-mouse Crp1 (Ayabe Lab clone 77-R63, 5 μg/mL, 50×) and rabbit anti-human Lyz (Dako, 200×) primary antibodies diluted to 10 μg/mL in staining solution (0.1% Triton X-100 and 10× Powerblock in PBSO) overnight at 4° C., followed by secondary antibodies Alexa Fluor 647 anti-Rabbit IgG (400×) and Alexa Fluor 488 anti-Rat IgG (400×) diluted in staining solution for 1 hour at RT. Actin was stained with Alexa Fluor 555 Phalloidin (40×) for 20 minutes, followed by staining of the nucleus with 3 μM DAPI for 5 minutes. Coverslips were mounted onto slides with Vectashield and imaged within 5 days using an Olympus FV2000 confocal microscope. Whole organoid confocal microscopy images were processed and analyzed using ImageJ. To determine the PC purity percentage, the ImageJ Point Picker plugin was used to count the number of nuclei to determine total number of cells and to count the number of DEFA- and LYZ-containing PCs across all z-slices. To investigate cell polarity in whole organoids, individual cells were selected using ImageJ and mean area intensity within selected cell areas was computed in each z-slice throughout the depth of the image across every channel imaged.

High-Resolution Single-Cell Imaging.

Cell clusters were harvested and rinsed (basal culture media 3×) to remove Matrigel as previously described. Isolated clusters were resuspended in TrypLE Express and incubated at 37° C. for 20 minutes to dissociate into single cells, then rinsed (basal culture media 2×) and resuspended in PBS containing magnesium and calcium. Pre-coated poly-L-lysine coverslips (Fisher Scientific) were placed into wells of a 24-well plate, a cell suspension containing approximately 50,000 cells per well was added to each well, and the plate was centrifuged at 700 rcf for 5 minutes. PBS supernatant was removed from the wells, and the cells attached to the coverslips were fixed by incubating with 4% PFA for 30 minutes at RT. After each step, cells were rinsed (PBS 2-5 min 3×). Cells were blocked and permeabilized by incubating at RT for 30 minutes with permeabilization solution and stained with for DEFA and LYZ by incubating with rat anti-mouse Crp1 and rabbit anti-human Lyz primary antibodies diluted in staining solution overnight at 4° C. Secondary antibodies Alexa Fluor 647 anti-Rabbit IgG and Alexa Fluor 488 anti-Rat IgG diluted in staining solution were incubated with the coverslips for 1 hour at RT. Actin was stained with Alexa Fluor 555 Phalloidin incubated for 20 minutes at RT, and the nucleus was stained with DAPI by incubating at RT for 5 mins. Coverslips were mounted on to slides with Vectashield and imaged within 48 hours using an Applied Precision DeltaVision Microscope.

Flow Cytometry.

Cell clusters were isolated from Matrigel as previously described and resuspended in TrypLE Express at 37° C. for 20 mins to dissociate into single cells. Dissociated cells were centrifuged at 300 g for 3 mins at 4° C. The pellet was resuspended in FACS buffer (1% FBS in PBS, Thermo Fisher Scientific) and strained into a 5-mL filter cap tube using a 40 m filter. The cell suspension was transferred to a flow prep microcentrifuge tube and centrifuged at 300 rcf for 3 min. Cell pellets were resuspended in a Zombie violet dye (BioLegend 100×) in FACS buffer for viability staining followed with 1% PFA fixation for 20 minutes at RT. Pellets were permeabilized for 20 minutes at RT with staining buffer (0.5% Tween-20 in FACS buffer, Sigma), and co-stained with rabbit anti-human FITC-Lyz (100×) and rat anti-mouse APC-CD24 (100×) antibodies diluted in staining buffer for 45 min at RT. Flow cytometry was performed using a BD LSR II HTS (BD; Koch Institute Flow Cytometry Core at MIT). Initial settings and laser voltages were determined with unstained, single channel stains or secondary-only controls (data not shown). Flow cytometry data was analyzed using FlowJo v10.7 software. Briefly, gating was performed as seen in FIG. 8F by removing doubles and debris, then selecting the BV421- (viable) cell population; within this population, gating was based on LYZ- and CD24-populations.

Lysozyme Functional Secretion Assay.

Lysozyme secretion was measured using a Lysozyme Assay Kit (EnzChek; Thermo Fisher). Briefly, cells suspended in Matrigel in 24-well plates were washed (basal culture media 3×) and either supplemented with 500 μL of basal culture media or basal culture media plus 10 μM Carbachol (CCh, Sigma Aldrich) for 24 hours at 37° C. Following stimulation, culture plates were spun at high speed (>2000 g) for 5 min at RT to pellet cell debris and loose Matrigel. 25 μL of conditioned supernatant was removed from the top of each well and quantified per manufacturer's protocol.

Quantification of Cell Viability, Apoptosis, Cytotoxicity.

To track proliferation and cell viability, DNA content was quantified over the course of differentiation and CCh-stimulation using a CyQUANT Cell Proliferation Assay Kit (Thermo Fisher) per manufacturer's protocol. Briefly, culture media was aspirated from each well, and the wells washed (PBS 3×). Gels were then mechanically dissociated into PBS, contents transferred into a Falcon tube, centrifuged at 300 rcf for 3 min at 4° C., and the pellet resuspended in PBS to wash. Tubes were centrifuged at 300 rcf for 5 min at 4° C., and the pellet resuspended in 1 mL assay working solution (20× cell-lysis buffer, 400× GR dye in DI water). 200 μL of samples and DNA standards were plated in triplicate in a black 96-well plate, shaken for 5 min, then fluorescence was measured on a plate reader (480 nm/520 nm).

For ENR/ENR+CD co-culture, ISC-enriched organoids (ENR+CV) were differentiated in ENR and ENR+CD and isolated as previously described. The cell pellets were counted and resuspended in basal culture medium, mixed at 0:100, 25:75, 50:50, 75:25, and 100:0% ENR:ENR+CD ratios (number of clusters), and plated as previously described in Matrigel in a 96-well plate at approximately 50 clusters/well in ENR media. After 24 and 48 hours of co-culture, viability versus cytotoxicity and caspase activation were assessed using ApoTox-Glo Triplex Assay (Promega) according to the manufacturer's protocol. Briefly, 20 μL of “V/C reagent” (10 L each of GF-AFC and bis-AAF-R110 substrates in 2.0 mL of assay buffer) were added to all wells and mixed by orbital shaking at 500 rpm for 30 sec. After 30 minutes of incubation at 37° C., fluorescence was measured on a plate reader (400 nm/505 nm for viability and 485 nm/520 nm for cytotoxicity). 100 μL of Caspase-Glo 3/7 reagent was then added to all wells and mixed by orbital shaking at 500 rpm for 30 sec. After 30 minutes of incubation at RT, luminescence was measured on a plate reader.

Bacteria Co-Culture.

For bacteria co-culture, ISC-enriched cells (ENR+CV) were differentiated in ENR and ENR+CD as previously described. After six days of differentiation, cell clusters were isolated as previously described. The cell pellet was resuspended in basal culture medium and plated in suspension in a 96-well plate at approximately 150 clusters/well. A 1:1 volume of bacteria in respective media (see “Bacterial strains,” above; in exponential growth, as confirmed by plate reader OD) was added, and bacterial growth was measured by serial plating (CFU) after a 4-hour incubation. Results for bacteria co-culture were normalized to no cell (bacteria only) controls.

Mass Spectrometry Proteomics Sample Preparation, Sequencing, and Quantification.

Organoid cell pellets were isolated from Matrigel with mechanical dissociation and washed (cold PBS 5×) to remove residual extracellular protein. Proteins were extracted from cell pellets with 8 M urea (Sigma), reduced with 5 mM DTT (Thermo Fisher Pierce) for 45 minutes, alkylated with 10 mM IAA (Sigma) for 45 minutes in the dark, and double digested with both Lysyl Endopeptidase “LysC” (Wako) and trypsin (Promega) overnight at RT. A small aliquot of cellular lysate was removed from each sample for protein quantification via the Pierce™ BCA Protein Assay Kit (Pierce). After proteolytic digestion, the samples were quenched using formic acid to a final concentration of 1.0% and subsequently desalted on 10 mg OASIS HLB solid phase columns (Waters).

From each condition (n=8), 50 μg aliquots of the Ng KD dried tryptic peptides were reconstituted in 100 mM HEPES pH 8.0 to a final concentration of 1.0 mg/mL. The peptides were labeled with TMT-10 isobaric mass tag reagent according to manufacturer's instructions (ThermoFisher Scientific). The peptides were labeled at a 1:8 ratio of peptide to TMT reagent, followed by 1-hour incubation at RT with bench top shaking at 850 rpm. After incubation, a 1.0 μg aliquot of labeled tryptic peptide was removed from each labeled condition, desalted with C18 stage tips, and analyzed via LC-MS/MS using a Thermo Fisher Q Exactive Plus Hybrid Mass Spectrometer (QE-Plus) coupled to a Thermo Fisher EASY-nLC 1000 liquid chromatograph to ensure isobaric label incorporation ≥95%. An additional 1.0 μg of labeled tryptic peptide was removed from each channel, mixed together, desalted on a C18 stage tip, and analyzed via LC-MS to ensure equal relative protein loads. During these quality control steps, the labeled peptides were stored, unquenched at −80° C. After validation, each channel was quenched with a 5% hydroxylamine solution to a final sample concentration of 0.3% to quench any unbound isobaric tags. The corresponding 8 channels were mixed together for a total amount of 400 μg of labeled tryptic peptides. The labeled peptide mixture was dried down in a speedvac and subsequently desalted on 30 mg OASIS HLB solid phase column (Waters).

The dried, labeled peptides were fractionated into 24 fractions by basic reversed-phase (bRP) using an Agilent Zorbax 300 Å 4.6 mm×250 mm Extend-C18 column on an Agilent 1100 Series HPLC instrument (Agilent Technologies) to decrease sample complexity and increase the dynamic range of detection. Solvent A (2% acetonitrile, 5 mM ammonium formate, pH 10), and a nonlinear increasing concentration of solvent B (90% acetonitrile, 5 mM ammonium formate, pH 10) was used as the mobile phase with a flow rate of 1 mL/min through the column. A nonlinear gradient with increasing percentages of solvent B with 4 different slopes was used (0% for 7 min; 0% to 16% in 6 min; 16% to 40% in 60 min; 40% to 44% in 4 min; 44% to 60% in 5 min; 60% for 14 min), and the eluted peptides were collected in a Whatman polypropylene 2 mL 96-well plate (Whatman). The 96 fractions were concatenated down to 25 fractions.

The global proteome (25 fractions) was analyzed by LC-MS/MS using the same system described above. Peptides were separated at a flow rate of 200 nL/min on a capillary column (Picofrit with a 10-μm tip opening and 75 m diameter, New Objective, PF360-75-10-N-5) packed at the Broad Institute with 20 cm of C18 1.9 m silica beads (1.9-μm ReproSil-Pur C18-AQ medium, Dr. Maisch GmbH, r119.aq). Injected peptides were separated at a flow rate of 200 nL/min with a linear 84-min gradient from 100% solvent A (3% acetonitrile, 0.1% formic acid) to 30% solvent B (90% acetonitrile, 0.1% formic acid), followed by a linear 9-min gradient from 30% solvent A to 90% solvent B for a total of 110 minutes. The QE-Plus instrument was operated in the data-dependent mode acquiring higher-energy collisional dissociation tandem mass spectrometry (HCD MS/MS) scans (Resolution=35,000) for TMT-10 on the 12 most abundant ions using an MS 1 ion target of 3×10⁶ ions and an MS2 target of 5×10⁴ ions. The maximum ion time used for the MS/MS scans was 120 ms; the HCD-normalized collision energy was set to 31; the dynamic exclusion time was set to 20 secs, and the peptide-match preferred setting was enabled.

Quality Control of Mass Spectrometry Performance and Data Generated.

Before running batches of samples, the liquid chromatography (LC) and mass spectrometer (MS) performance (retention time, chromatographic peak width, sensitivity, signal-to-noise, and mass accuracy) were verified by analyzing a reference material (a mixture of 5-7 standard peptides). Applicants have implemented calculation of the primary NIST LC-MS/MS metrics [65] into Spectrum Mill (SM) to monitor ongoing system performance quality when analyzing samples. Specific metrics measure: enzyme cleavage fidelity, deamidation, carbamylation, chromatographic peak width, relative dynamic sampling of MS/MS near the chromatographic apex, the portion of the LC gradient over which peptides are identified, distribution of precursor charges, mass accuracy, portion of collected MS/MS that are identifiable, distribution of peptide pI (for IEF based separations) and/or solution charge (for SCX based separations), certainty in localization of phosphorylation sites, variability in peptide/protein quantification, and FDR for peptide/protein identification.

Protein and Peptide Identification and Quantification.

Peptide spectrum matching and protein identification was performed using Agilent Technologies SM software package (developed at the Broad Institute). In SM, false discovery rates (FDRs) are calculated at three different levels: spectrum, distinct peptide, and distinct protein. Peptide FDRs are calculated in SM using essentially the same pseudo-reversal strategy evaluated by Elias and Gygi [66] and shown to perform the same as library concatenation. A false distinct protein ID occurs when all the distinct peptides that group together to constitute a distinct protein have a deltaForwardReverseScore ≤0. Applicants adjust settings to provide peptide FDR of 1-2% and protein FDR of 0-1%. SM also carries out sophisticated protein grouping using the methods previously described [67]. Only proteins with >2 peptides and at least 2 TMT ratios in each replicate are counted as being identified and quantified. Additionally, Applicants added the capability to flag potentially unreliable TMT quantification results based on detection of more than one precursor in the selection window for MS/MS. The precursor ion flagging is similar to that recently reported [68] but is carried out post-data acquisition. As an output, SM generates protein and peptide reports for downstream differential regulation, pathway, and network analysis. Prior to comprehensive differential marker, pathway, and network analysis with the SM generated protein reports, Applicants ensure that the data is of high quality and has been properly normalized. The first level of normalization is accomplished by guaranteeing that equivalent amount of peptide (50 μg per) is labeled for each of the 10 TMT channels. Once the SM reports are generated, Applicants calculate the median ratios for each of the channels where the denominator of the ratio is a predetermined TMT channel signifying the control condition. The underlying assumption is that the null distribution is centered at zero in log 2 space. Therefore, in this step of normalization, Applicants normalize the median log 2 ratio for each ratio column so that the median log 2 ratio is zero. To robustly and confidently detect real differential peptides and proteins in the TMT-labeled experiment, Applicants performed a moderated t-test [69,70]. Unlike the standard t-test, which is not robust for small numbers of samples, the moderated t-test uses an empirical Bayes approach that “moderates” variance estimates for peptides (i.e., shrunk towards a common value), thereby significantly improving the stability of variance estimates for individual peptides. The p-values reported by the moderated t-test are adjusted for multiple testing using the Benjamini-Hochberg FDR method [70]. Additionally, Venn diagrams showing sample overlap were produced with Venny 2.0 software [71].

Proteome Pathway and Network Analysis.

Using the identified and quantified proteins from the TMT-10 labeling experiment, multiple pathway and network analyses were performed. Sample correlations were represented as r-values and determined using GraphPad Prism version 7.0a. To assess sample variability, Applicants computed the median-normalized relative abundance of each protein identified as significantly enriched (from the median-normalized ratio of ENR+CD/ENR paired samples) within the four ENR+CD samples and four ENR samples, and calculated the coefficient of variation (CoV) (sample standard deviation over mean) for each protein across the four samples. To assess proteome enrichment for a standard Paneth cell gene set, Applicants rank-ordered all 8,015 detected proteins, and used GSEA v3.0b2 [39,40] “Preranked” to compute set enrichment against a gene set of the top 500 genes differentially regulated in a microarray comparison of in vivo Paneth cells versus LRG5+ ISCs performed by [16]. To elucidate potential transcriptional drivers of proteome structure, Applicants performed GSEA using the full rank-ordered proteome against the transcription factor target gene set database (v5.2 MSigDB) [41], then performed enrichment map visualization using GSEA-P-based implementation and Cytoscape v3.4.0 [42,43] with a moderately conservative cutoff (p-value <0.005 and FDR<0.075) and an overlap coefficient of 0.2. To assess the functional and compartmental functions associated with the ENR+CD-enriched proteome and ENR-enriched proteome, Applicants used DAVID v6.8 [72,73] and the gene ontology (GO) database, looking only at experimentally verified associations within biological processes (BP), cellular compartments (CC), and molecular function (MF) against a background set of all 8,015 quantified proteins.

Single-Cell RNA-Sequencing.

A single-cell suspension was obtained from organoids cultured under ENR+CV, ENR, and ENR+CD conditions for six days as described above. Applicants utilized the Seq-Well platform for massively parallel scRNA-seq to capture transcriptomes of single cells on barcoded mRNA capture beads. Full methods on implementation of this platform are available in [31]. In brief, 20,000 cells from one organoid condition were loaded onto one array containing 100,000 barcoded mRNA capture beads. The loaded arrays containing cells and beads were then sealed using a polycarbonate membrane with a pore size of 0.01 μm, which allows for exchange of buffers but retains biological molecules confined within each microwell. Subsequent exchange of buffers allows for cell lysis, transcript hybridization, and bead recovery before performing reverse transcription en masse. Following reverse transcription and exonuclease treatment to remove excess primers, PCR amplification was carried out using KAPA HiFi PCR Mastermix with 2,000 beads per 50 μL reaction volume. Six libraries (totaling 12,000 beads) were then pooled and purified using Agencourt AMPure XP beads (Beckman Coulter, A63881) by a 0.6×SPRI followed by a 0.7×SPRI and quantified using Qubit hsDNA Assay (Thermo Fisher). Libraries were constructed using the Nextera Tagmentation method on a total of 800 pg of pooled cDNA library from 12,000 recovered beads. Tagmented and amplified sequences were purified at a 0.6×SPRI ratio yielding library sizes with an average distribution of 650-750 base pairs in length as determined using the Agilent hsD1000 Screen Tape System (Agilent Genomics). Arrays were sequenced with an Illumina 75 Cycle NextSeq500/550v2 kit at a final concentration of 2.8 pM. The read structure was paired end with Read 1 starting from a custom read 1 primer containing 20 bases with a 12 bp cell barcode and 8 bp unique molecular identifier (UMI) and Read 2 being 50 bases containing transcript information.

Single-Cell RNA-Sequencing Computational Pipelines and Analysis.

Read alignment was performed as in [74]. Briefly, for each NextSeq sequencing run, raw sequencing data was converted to demultiplexed FASTQ files using bcl2fastq2 based on Nextera N700 indices corresponding to individual samples/arrays. Reads were then aligned to mm10 genome using the Galaxy portal maintained by the Broad Institute for Drop-Seq alignment using standard settings. Individual reads were tagged according to the 12-bp barcode sequencing and the 8-bp UMI contained in Read 1 of each fragment. Following alignment, reads were binned onto 12-bp cell barcodes and collapsed by their 8-bp UMI. Digital gene expression matrices (e.g. cell by gene tables) for each sample were obtained from quality filtered and mapped reads and UMI-collapsed data, are deposited in GSE100274, and were utilized as input into Seurat [75] and github.com/satijalab/seurat] for further analysis.

To analyze ENR+CV, ENR, and ENR+CD organoids together, Applicants merged UMI matrices across all genes detected in any condition and generated a matrix retaining all cells with at least 1000 UMI detected. This table was then utilized to setup the Seurat object in which any cell with at least 400 unique genes was retained and any gene expressed in at least 5 cells was retained. The object was initiated with log-normalization, scaling, and centering set to True. Before performing dimensionality reduction, data was subset to include cells with less than 8,000 UMI, and a list of 1,676 most variable genes was generated by including genes with an average normalized and scaled expression value greater than 0.14 and with a dispersion (variance/mean) greater than 0.4. The total number of ENR+CV, ENR, and ENR+CD cells included in the analysis was 985, 2,544, and 2,382, respectively with quality metrics for nGene, nUMI, and percentage of ribosomal and mitochondrial genes reported in FIG. 11. Applicants then performed principal component analysis over the list of variable genes. For both clustering and t-stochastic neighbor embedding (tSNE), Applicants utilized the first 12 principal components based on the elbow method, as upon visual inspection of genes contained within, each contributed to important biological processes of intestinal cells. Applicants used FindClusters with a resolution of 1.35 and 1000 iterations of tSNE to identify 14 clusters across the 3 input samples. To identify genes which defined each cluster, Applicants performed a ROC test implemented in Seurat with a threshold set to an AUC of 0.60.

Transcriptional Scoring. To determine the fractional contribution to a cell's transcriptome of a gene list, Applicants summed the total log(scaled UMI+1) expression values for genes within a list of interest and divided by the total amount of scaled UMI detected in that cell giving a proportion of a cell's transcriptome dedicated to producing those genes. From the proteomic screen, Applicants took a list of upregulated proteins (249) or downregulated proteins (212) that were detected within the single-cell RNA-sequencing data. To determine the relationship to in vivo Paneth cells and EECs, Applicants took reference data from two Seq-Well experiments run on epithelial cells dissociated from the ileal region of the small intestine of two C57BL/6J mice run in separate experiments. Ileum was first rinsed in 30 mL of ice cold PBS and allowed to settle. The segment was then sliced with scissors and transferred to 10 mL epithelial cell solution (HBSS Ca/Mg-Free 10 mM EDTA, 100 U/mL penicillin, 100 μg/mL streptomycin, 10 mM HEPES, 2% FCS (ThermoFisher)) freshly supplemented with 200 μL of 0.5 M EDTA. The epithelial separation from the underlying lamina propria was performed for 15 minutes at 37° C. in a rotisserie rack with end-over-end rotation. The tube was then removed and placed on ice immediately for 10 minutes before shaking vigorously 15 times. Visual macroscopic inspection of the tube at this point should yield visible epithelial sheets, and microscopic examination confirms the presence of single-layer sheets and crypt-villus structures. The epithelial fraction was spun down at 400 g for 7 minutes and resuspended in 1 mL of epithelial cell solution before transferring to a 1.5 mL Eppendorf tube to minimize time spent centrifuging. Cells were spun down at 800 g for 2 minutes and resuspended in TrypLE Express for 5 minutes in a 37° C. bath followed by gentle trituration with a P1000 pipette. Cells were spun down at 800 g for 2 minutes and resuspended in ACK lysis buffer (ThermoFisher) for 3 minutes on ice to remove red blood cells and dying cells. Cells were spun down at 800 g for 2 minutes and resuspended in 1 mL of epithelial cell solution and placed on ice for 3 minutes before triturating with a P1000 pipette and filtering into a new Eppendorf through a 40 m cell strainer (Falcon/VWR). Cells were spun down at 800 g for 2 minutes and then resupended in 200 μL of epithelial cell solution and placed on ice for counting. Single-cell RNA-seq data was then generated as described in (Single-cell RNA-sequencing and Single-cell RNA-sequencing computational pipelines and analysis) sections of methods. To generate Paneth and EEC signatures, Applicants ran unbiased SNN-graph based clustering, performed a ROC test, identified the two mature Paneth and EEC clusters, and report all genes with an AUC above 0.60, and use all genes with an AUC above 0.65 for scoring, within each cluster (gene lists in Table Si) representing any gene with enrichment in Paneth and EE cells. These lists capture genes which are enriched in Paneth (Lyz-high) and EE (Chga-high) cells, and separate them from the rest of the cells present in intestinal epithelium. For pathway analysis, Applicants inspected curated gene lists deposited in the GSEA platform and used KEGG-derived Wnt and Reactome-derived Notch and Respiratory Electron Transport Chain signatures (Table 2).

Quantification and statistical analysis. Statistical analyses were performed using GraphPad Prism v7.0a, Seurat implemented in RStudio, and Agilent Technologies Spectrum Mill software package. All graphs show mean±SEM, unless otherwise noted. Unpaired 2-tail t-test and 2-way ANOVA with Dunnett's multiple comparison test (reported as adj. p value) were used to assess statistical significance as appropriate and unless otherwise noted (* indicates p<0.05, ** p<0.01 *** p<0.001, **** p<0.0001, and ns non-significant). In each experiment, tissues were isolated from multiple mice housed in the same facility with each mouse providing tissue designated as a distinct biological donor: n=3 donor-averaged values of four technical replicates for data reported in FIG. 2B; n=3 donor of two technical replicates for data reported in FIG. 2E and FIG. 8F; n=4 (2 technical replicates from two biological donors each) for data reported in FIGS. 3, 9, and 10; n=1 biological donor for in vitro data reported in FIGS. 4-5 and 11-12; n=8 single-well replicates from one and five biological donors for data reported in FIGS. 6A-B and 6C, respectively; n=13 co-culture well replicates randomly selected without replacement from 4 donors for data reported in FIG. 6D; n=6 well replicates (2 per 3 biological donors) in FIG. 6E; n=3 biological donors in FIGS. 7C-D.

TABLE 1 Derived gene list of the top defining genes from in vivo ileal small intestine PCs and EECs captured on the Seq-Well platform Table 1A. Results of ROC-test for Paneth-enriched marker genes from all in vivo isolated small intestinal epithelial cells (FIG. 1C Paneth InVivo) myAUC avg_diff power pct.1 pct.2 cluster gene Gm1485110 0.998 3.54974509 0.996 1 0.248 11 Gm14851 Defa248 0.998 3.310135059 0.996 1 0.749 11 Defa24 Gm1528411 0.997 3.376627144 0.994 1 0.522 11 Gm15284 Defa1710 0.996 3.272012679 0.992 1 0.242 11 Defa17 Itln110 0.996 3.205344786 0.992 1 0.492 11 Itln1 Defa2210 0.995 3.488570378 0.99 1 0.276 11 Defa22 Lyz110 0.995 3.449655842 0.99 1 0.487 11 Lyz1 Defa2110 0.993 3.476885473 0.986 1 0.295 11 Defa21 Defa265 0.992 3.330019381 0.984 0.994 0.129 11 Defa26 Defa-rs12 0.992 3.295903275 0.984 0.997 0.092 11 Defa-rs1 Ang410 0.99 3.013942122 0.98 1 0.381 11 Ang4 AY76118410 0.989 3.35421008 0.978 0.997 0.213 11 AY761184 Defa38 0.989 3.064599256 0.978 0.994 0.117 11 Defa3 Gm153151 0.977 2.986060661 0.954 0.974 0.067 11 Gm15315 Clps3 0.977 2.850671309 0.954 0.974 0.091 11 Clps Gm101041 0.976 2.924572319 0.952 0.971 0.057 11 Gm10104 Gm152921 0.97 2.78093711 0.94 0.966 0.078 11 Gm15292 Mmp72 0.969 2.732627523 0.938 0.966 0.095 11 Mmp7 AY7611851 0.953 2.902034038 0.906 0.925 0.046 11 AY761185 Reg41 0.951 2.7690051 0.902 0.934 0.086 11 Reg4 Pnliprp22 0.936 2.515088835 0.872 0.911 0.092 11 Pnliprp2 Gm152991 0.936 2.478413248 0.872 0.897 0.045 11 Gm15299 Spink410 0.93 1.510850666 0.86 1 0.567 11 Spink4 Defa-rs71 0.921 2.634772041 0.842 0.862 0.033 11 Defa-rs7 Ccl69 0.899 1.857462818 0.798 0.885 0.125 11 Ccl6 Gm148501 0.897 2.286355764 0.794 0.816 0.028 11 Gm14850 Gm152931 0.891 2.193886938 0.782 0.802 0.025 11 Gm15293 Mptx21 0.883 3.092439953 0.766 0.816 0.083 11 Mptx2 Lyz21 0.837 1.794805054 0.674 0.701 0.028 11 Lyz2 Nupr11 0.833 1.766838324 0.666 0.704 0.043 11 Nupr1 Cd24a5 0.832 1.202885956 0.664 0.799 0.174 11 Cd24a Defa5 0.817 1.993723258 0.634 0.644 0.01 11 Defa5 Lars2 0.804 1.01036761 0.608 0.899 0.551 11 Lars2 Defa23 0.792 2.141723321 0.584 0.598 0.013 11 Defa23 Gm155641 0.791 1.070350926 0.582 0.83 0.385 11 Gm15564 Gm7861 0.76 1.463726478 0.52 0.529 0.007 11 Gm7861 Defa20 0.739 1.746076506 0.478 0.483 0.005 11 Defa20 Gm21498 0.73 1.275479302 0.46 0.466 0.006 11 Gm21498 Lbh 0.728 1.236030548 0.456 0.489 0.03 11 Lbh Gm6696 0.714 1.151645801 0.428 0.437 0.007 11 Gm6696 Gm21002 0.709 1.303327251 0.418 0.422 0.004 11 Gm21002 Defa2 0.703 1.220649508 0.406 0.411 0.004 11 Defa2 Gm15308 0.703 1.079396917 0.406 0.414 0.006 11 Gm15308 Mptx12 0.696 1.376763812 0.392 0.457 0.064 11 Mptx1 Rnase44 0.689 0.671704918 0.378 0.592 0.22 11 Rnase4 Tmed6 0.688 0.934851402 0.376 0.394 0.018 11 Tmed6 Habp2 0.687 1.004624823 0.374 0.379 0.006 11 Habp2 Gm7849 0.675 1.028781992 0.35 0.353 0.002 11 Gm7849 Nucb21 0.675 0.886781076 0.35 0.371 0.02 11 Nucb2 Ggh 0.667 0.823103237 0.334 0.356 0.021 11 Ggh Qsox12 0.666 0.693239013 0.332 0.434 0.095 11 Qsox1 Tspan16 0.665 0.515819615 0.33 0.572 0.227 11 Tspan1 Tmprss22 0.659 0.676826722 0.318 0.422 0.101 11 Tmprss2 mmu-mir-6236 0.658 0.522921887 0.316 0.552 0.216 11 mmu-mir-6236 Ramp12 0.655 0.689299748 0.31 0.376 0.059 11 Ramp1 Bambi 0.648 0.861536976 0.296 0.305 0.008 11 Bambi Gm97651 0.643 1.066347908 0.286 0.313 0.025 11 Gm9765 Ang5 0.641 0.722917045 0.282 0.293 0.01 11 Ang5 Smim142 0.639 0.37355984 0.278 0.46 0.161 11 Smim14 Wbp57 0.636 0.356539074 0.272 0.48 0.181 11 Wbp5 Car81 0.635 0.597328844 0.27 0.319 0.046 11 Car8 Asph2 0.635 0.562816272 0.27 0.356 0.081 11 Asph Tram12 0.633 0.479273876 0.266 0.517 0.248 11 Tram1 Fam46c 0.626 0.620047992 0.252 0.261 0.008 11 Fam46c Ly6e1 0.622 0.500854668 0.244 0.316 0.067 11 Ly6e Olfm47 0.622 0.328982619 0.244 0.425 0.162 11 Olfm4 5330417C22Rik2 0.62 0.500934933 0.24 0.305 0.059 11 5330417C22Rik Slc12a28 0.618 0.321997521 0.236 0.457 0.195 11 Slc12a2 Dnajc32 0.615 0.360035595 0.23 0.497 0.256 11 Dnajc3 Sox92 0.611 0.523456428 0.222 0.282 0.056 11 Sox9 Hpd1 0.609 0.555541502 0.218 0.239 0.019 11 Hpd Gadd45g 0.608 0.504412695 0.216 0.287 0.067 11 Gadd45g Ang1 0.608 0.496801656 0.216 0.282 0.063 11 Ang Reep51 0.607 0.360389211 0.214 0.259 0.04 11 Reep5 Sypl5 0.604 0.27513369 0.208 0.5 0.274 11 Sypl Ang6 0.603 0.528311205 0.206 0.213 0.006 11 Ang6 Trp53inp1 0.601 0.527522118 0.202 0.218 0.016 11 Trp53inp1 Table 1B. ROC-test on conventional ENR organoids to determine cluster-enriched marker genes (FIG. 1E Paneth ENR-4) myAUC avg_diff power pct.1 pct.2 cluster gene Defa24 0.954 2.171101878 0.908 0.998 0.912 ENR-4 Defa24 Defa17 0.947 2.17783303 0.894 0.992 0.669 ENR-4 Defa17 Gm15284 0.916 2.280079164 0.832 0.982 0.633 ENR-4 Gm15284 Spink4 0.914 1.711003544 0.828 0.997 0.747 ENR-4 Spink4 Clps 0.885 1.862014447 0.77 0.9 0.305 ENR-4 Clps Itln1 0.882 2.101891237 0.764 0.946 0.552 ENR-4 Itln1 Tff3 0.864 1.457124813 0.728 0.969 0.602 ENR-4 Tff3 Lyz1 0.856 1.976178002 0.712 0.91 0.457 ENR-4 Lyz1 Gm14851 0.854 2.07922191 0.708 0.834 0.236 ENR-4 Gm14851 Defa-rs1 0.838 1.979555244 0.676 0.783 0.184 ENR-4 Defa-rs1 AY761184 0.837 2.028401106 0.674 0.819 0.245 ENR-4 AY761184 Gm15299 0.804 1.722132795 0.608 0.706 0.149 ENR-4 Gm15299 Guca2a 0.77 1.343910845 0.54 0.723 0.254 ENR-4 Guca2a Ang4 0.765 1.902429314 0.53 0.656 0.188 ENR-4 Ang4 Defa3 0.762 1.625202786 0.524 0.608 0.119 ENR-4 Defa3 Defa26 0.761 1.501994758 0.522 0.62 0.128 ENR-4 Defa26 AY761185 0.76 1.546633485 0.52 0.607 0.122 ENR-4 AY761185 Mmp7 0.76 1.517042969 0.52 0.643 0.173 ENR-4 Mmp7 Agr2 0.753 1.172849401 0.506 0.76 0.392 ENR-4 Agr2 Defa21 0.726 1.61303835 0.452 0.517 0.078 ENR-4 Defa21 Gm15315 0.682 1.46990469 0.364 0.418 0.063 ENR-4 Gm15315 Fcgbp 0.672 1.160467398 0.344 0.488 0.167 ENR-4 Fcgbp Gm10104 0.67 1.334688224 0.34 0.38 0.046 ENR-4 Gm10104 Defa22 0.668 1.525928795 0.336 0.398 0.071 ENR-4 Defa22 Defa23 0.665 1.184665633 0.33 0.369 0.043 ENR-4 Defa23 Gm14850 0.623 1.082882852 0.246 0.271 0.028 ENR-4 Gm14850 Klk1 0.618 0.865184481 0.236 0.305 0.074 ENR-4 Klk1 Rnase4 0.618 0.71009465 0.236 0.4 0.177 ENR-4 Rnase4 Cd24a 0.609 0.395125457 0.218 0.639 0.472 ENR-4 Cd24a Guca2b 0.605 0.522266578 0.21 0.346 0.135 ENR-4 Guca2b Ccl6 0.603 0.992561968 0.206 0.253 0.05 ENR-4 Ccl6 Ccl9 0.601 0.95781627 0.202 0.248 0.051 ENR-4 Ccl9 Fabp1 0.811 1.96298575 0.622 0.789 0.28 ENR-3 Fabp1 Aldob 0.785 1.2268382 0.57 0.892 0.572 ENR-3 Aldob Sis 0.756 1.48058628 0.512 0.689 0.237 ENR-3 Sis Prap1 0.737 1.104136722 0.474 0.768 0.435 ENR-3 Prap1 Mt1 0.699 0.5895937 0.398 0.963 0.885 ENR-3 Mt1 Adh1 0.693 1.158484368 0.386 0.533 0.178 ENR-3 Adh1 Reg1 0.681 1.91335161 0.362 0.449 0.104 ENR-3 Reg1 Fabp2 0.676 0.671558173 0.352 0.862 0.688 ENR-3 Fabp2 2210404O07Rik 0.669 0.792083339 0.338 0.675 0.406 ENR-3 2210404O07Rik Gsta1 0.655 1.27693185 0.31 0.384 0.082 ENR-3 Gsta1 Apoa1 0.653 1.312903918 0.306 0.382 0.085 ENR-3 Apoa1 Mt2 0.649 0.412988151 0.298 0.892 0.782 ENR-3 Mt2 Spink3 0.639 1.032180742 0.278 0.329 0.051 ENR-3 Spink3 Dbi 0.638 0.408183411 0.276 0.913 0.829 ENR-3 Dbi Khk 0.637 0.786298444 0.274 0.453 0.201 ENR-3 Khk Apoa4 0.627 1.202209448 0.254 0.313 0.063 ENR-3 Apoa4 Fth1 0.624 0.369737625 0.248 0.888 0.789 ENR-3 Fth1 Apoc3 0.622 1.099829904 0.244 0.285 0.044 ENR-3 Apoc3 Slc5a1 0.621 0.812338448 0.242 0.388 0.165 ENR-3 Slc5a1 Phgr1 0.62 0.33204232 0.24 0.833 0.698 ENR-3 Phgr1 Dak 0.619 0.739659127 0.238 0.425 0.209 ENR-3 Dak 2200002D01Rik 0.614 0.553046643 0.228 0.492 0.287 ENR-3 2200002D01Rik Leap2 0.607 0.945169933 0.214 0.258 0.046 ENR-3 Leap2 Mttp 0.606 0.676001129 0.212 0.319 0.115 ENR-3 Mttp Rbp2 0.601 0.77439673 0.202 0.24 0.04 ENR-3 Rbp2 Hsp90ab1 0.698 0.334241713 0.396 0.996 0.937 ENR-1 Hsp90ab1 Myh9 0.675 0.409130665 0.35 0.762 0.332 ENR-1 Myh9 Hook1 0.67 0.364663341 0.34 0.891 0.473 ENR-1 Hook1 Cdca7 0.659 0.334855426 0.318 0.638 0.234 ENR-1 Cdca7 Hspa8 0.659 0.290871832 0.318 0.985 0.771 ENR-1 Hspa8 Myb 0.658 0.360067147 0.316 0.491 0.133 ENR-1 Myb Smc3 0.658 0.340833172 0.316 0.57 0.193 ENR-1 Smc3 Npm1 0.658 0.276110838 0.316 0.985 0.794 ENR-1 Npm1 Rbbp4 0.658 0.269846162 0.316 0.675 0.254 ENR-1 Rbbp4 Olfm4 0.657 0.545651489 0.314 0.872 0.6 ENR-1 Olfm4 Gmnn 0.657 0.380979899 0.314 0.558 0.19 ENR-1 Gmnn Tpr 0.657 0.329120992 0.314 0.691 0.29 ENR-1 Tpr Sfpq 0.657 0.282887682 0.314 0.725 0.3 ENR-1 Sfpq Clca4 0.656 0.454481479 0.312 0.853 0.551 ENR-1 Clca4 Cps1 0.656 0.33978679 0.312 0.932 0.569 ENR-1 Cps1 Ehf 0.656 0.325039493 0.312 0.691 0.283 ENR-1 Ehf Fus 0.656 0.300083245 0.312 0.725 0.304 ENR-1 Fus Bzw1 0.655 0.347160369 0.31 0.709 0.311 ENR-1 Bzw1 Dhx9 0.655 0.280910067 0.31 0.619 0.224 ENR-1 Dhx9 Hspd1 0.653 0.30016784 0.306 0.928 0.566 ENR-1 Hspd1 Lbr 0.65 0.326705408 0.3 0.596 0.225 ENR-1 Lbr Sdc4 0.649 0.269766391 0.298 0.664 0.265 ENR-1 Sdc4 Smoc2 0.648 0.3369791 0.296 0.747 0.352 ENR-1 Smoc2 Baz1b 0.648 0.283798796 0.296 0.543 0.186 ENR-1 Baz1b G3bp1 0.648 0.25867788 0.296 0.649 0.255 ENR-1 G3bp1 Otc 0.648 0.25350988 0.296 0.638 0.255 ENR-1 Otc Nedd4 0.647 0.322402778 0.294 0.823 0.426 ENR-1 Nedd4 Fkbp3 0.647 0.289611023 0.294 0.83 0.456 ENR-1 Fkbp3 Naa50 0.647 0.285354396 0.294 0.543 0.186 ENR-1 Naa50 Caprin1 0.647 0.266494852 0.294 0.664 0.278 ENR-1 Caprin1 Mki67 0.646 0.393499983 0.292 0.687 0.359 ENR-1 Mki67 Sae1 0.646 0.330549185 0.292 0.558 0.205 ENR-1 Sae1 Hnrnpu 0.646 0.299131548 0.292 0.906 0.528 ENR-1 Hnrnpu Hnrnpa2b1 0.646 0.277900834 0.292 0.958 0.716 ENR-1 Hnrnpa2b1 Bzw2 0.645 0.316393214 0.29 0.626 0.258 ENR-1 Bzw2 Srrm1 0.645 0.292826665 0.29 0.623 0.261 ENR-1 Srrm1 Naa15 0.645 0.280446006 0.29 0.506 0.162 ENR-1 Naa15 Nop58 0.645 0.270458021 0.29 0.77 0.376 ENR-1 Nop58 Ncl 0.644 0.268323897 0.288 0.992 0.834 ENR-1 Ncl Hjurp 0.643 0.282338669 0.286 0.521 0.177 ENR-1 Hjurp Ywhab 0.643 0.266608555 0.286 0.642 0.27 ENR-1 Ywhab Ewsr1 0.642 0.31223685 0.284 0.54 0.198 ENR-1 Ewsr1 Bclaf1 0.642 0.268926732 0.284 0.611 0.245 ENR-1 Bclaf1 Tra2b 0.642 0.268817853 0.284 0.558 0.2 ENR-1 Tra2b Prdx4 0.642 0.264527859 0.284 0.562 0.21 ENR-1 Prdx4 Sypl 0.641 0.271683218 0.282 0.713 0.325 ENR-1 Sypl Slc12a2 0.64 0.293751642 0.28 0.879 0.5 ENR-1 Slc12a2 Cct2 0.64 0.263489435 0.28 0.785 0.38 ENR-1 Cct2 Ptma 0.639 0.283084487 0.278 0.97 0.712 ENR-1 Ptma Nap1l1 0.639 0.267612422 0.278 0.592 0.233 ENR-1 Nap1l1 Ifitm3 0.639 0.260879559 0.278 0.615 0.255 ENR-1 Ifitm3 Ccnd1 0.638 0.290978798 0.276 0.521 0.188 ENR-1 Ccnd1 Hmgn1 0.638 0.284595319 0.276 0.819 0.452 ENR-1 Hmgn1 Sf3b2 0.638 0.271204506 0.276 0.574 0.23 ENR-1 Sf3b2 Usp1 0.636 0.272893787 0.272 0.498 0.174 ENR-1 Usp1 Khdrbs1 0.635 0.270282197 0.27 0.438 0.13 ENR-1 Khdrbs1 Lsm5 0.635 0.264283642 0.27 0.442 0.13 ENR-1 Lsm5 Pa2g4 0.634 0.293891929 0.268 0.853 0.509 ENR-1 Pa2g4 Zfp292 0.634 0.276209814 0.268 0.547 0.218 ENR-1 Zfp292 Set 0.634 0.268891816 0.268 0.694 0.325 ENR-1 Set Serbp1 0.634 0.26379132 0.268 0.955 0.723 ENR-1 Serbp1 Plcb3 0.633 0.263428885 0.266 0.638 0.274 ENR-1 Plcb3 Top2a 0.631 0.386782218 0.262 0.664 0.364 ENR-1 Top2a Uchl5 0.631 0.273390369 0.262 0.411 0.117 ENR-1 Uchl5 Shmt2 0.631 0.25849999 0.262 0.46 0.149 ENR-1 Shmt2 Zfp326 0.63 0.391592517 0.26 0.351 0.075 ENR-1 Zfp326 Smchd1 0.63 0.349892312 0.26 0.396 0.109 ENR-1 Smchd1 Smc4 0.63 0.300538359 0.26 0.615 0.293 ENR-1 Smc4 Nudc 0.63 0.286242444 0.26 0.419 0.124 ENR-1 Nudc Mcm7 0.627 0.261145303 0.254 0.442 0.146 ENR-1 Mcm7 Lgr5 0.626 0.281390771 0.252 0.445 0.153 ENR-1 Lgr5 Rrm1 0.625 0.283364925 0.25 0.475 0.18 ENR-1 Rrm1 Aqp4 0.625 0.267685021 0.25 0.438 0.145 ENR-1 Aqp4 Tsix 0.624 0.311631552 0.248 0.374 0.1 ENR-1 Tsix Smarca5 0.624 0.263274671 0.248 0.468 0.174 ENR-1 Smarca5 2810417H13Rik 0.623 0.322764824 0.246 0.57 0.268 ENR-1 2810417H13Rik Smarca4 0.623 0.318678776 0.246 0.46 0.169 ENR-1 Smarca4 Hat1 0.621 0.289215145 0.242 0.396 0.123 ENR-1 Hat1 Dnajc9 0.619 0.263494313 0.238 0.411 0.138 ENR-1 Dnajc9 Xist 0.619 0.260299383 0.238 0.921 0.705 ENR-1 Xist Zfp36l2 0.619 0.253757487 0.238 0.423 0.146 ENR-1 Zfp36l2 Mrps5 0.618 0.267493357 0.236 0.374 0.111 ENR-1 Mrps5 Fnbp1l 0.618 0.257135033 0.236 0.404 0.134 ENR-1 Fnbp1l Cenpe 0.617 0.316507736 0.234 0.411 0.148 ENR-1 Cenpe Mrpl19 0.617 0.262521642 0.234 0.355 0.097 ENR-1 Mrpl19 Prim1 0.617 0.255494095 0.234 0.396 0.132 ENR-1 Prim1 Zbtb38 0.615 0.290816135 0.23 0.351 0.099 ENR-1 Zbtb38 Atic 0.615 0.265040334 0.23 0.381 0.119 ENR-1 Atic Tpx2 0.614 0.379022789 0.228 0.332 0.087 ENR-1 Tpx2 Wwp1 0.61 0.283271291 0.22 0.336 0.096 ENR-1 Wwp1 Pold3 0.61 0.272431026 0.22 0.302 0.067 ENR-1 Pold3 Cdca3 0.609 0.280047233 0.218 0.423 0.169 ENR-1 Cdca3 AI747448 0.608 0.266683788 0.216 0.457 0.198 ENR-1 AI747448 Wasf2 0.608 0.251327648 0.216 0.351 0.109 ENR-1 Wasf2 Smc2 0.607 0.289369633 0.214 0.442 0.189 ENR-1 Smc2 Suclg2 0.604 0.252788739 0.208 0.347 0.111 ENR-1 Suclg2 Fam98b 0.602 0.294037917 0.204 0.279 0.062 ENR-1 Fam98b Topbp1 0.601 0.279548647 0.202 0.317 0.096 ENR-1 Topbp1 Chgb 0.964 3.091633248 0.928 0.989 0.328 Neuro-2 Chgb Chga 0.88 2.943854249 0.76 0.818 0.114 Neuro-2 Chga Tac1 0.843 2.431672411 0.686 0.761 0.136 Neuro-2 Tac1 Reg41 0.841 3.285182681 0.682 0.818 0.369 Neuro-2 Reg4 Afp 0.788 3.531645662 0.576 0.602 0.048 Neuro-2 Afp Tph1 0.771 2.073030929 0.542 0.557 0.02 Neuro-2 Tph1 Sepp1 0.765 1.704289699 0.53 0.636 0.155 Neuro-2 Sepp1 Gstt1 0.706 1.591833899 0.412 0.466 0.073 Neuro-2 Gstt1 S100a1 0.698 1.623168802 0.396 0.455 0.078 Neuro-2 S100a1 Cystm1 0.681 0.693905241 0.362 0.807 0.629 Neuro-2 Cystm1 Me2 0.679 1.346412804 0.358 0.466 0.162 Neuro-2 Me2 Rab3c 0.676 1.608459983 0.352 0.364 0.014 Neuro-2 Rab3c Resp18 0.668 1.368961996 0.336 0.364 0.03 Neuro-2 Resp18 Pcsk1 0.665 1.533187939 0.33 0.364 0.041 Neuro-2 Pcsk1 Ctsl 0.65 0.966768573 0.3 0.364 0.071 Neuro-2 Ctsl Tpbg 0.648 1.266163184 0.296 0.307 0.012 Neuro-2 Tpbg Ddc 0.648 1.073792267 0.296 0.386 0.104 Neuro-2 Ddc Cd63 0.646 0.600552027 0.292 0.625 0.4 Neuro-2 Cd63 Vim 0.641 1.253503003 0.282 0.307 0.026 Neuro-2 Vim Rgs2 0.639 1.346366867 0.278 0.295 0.02 Neuro-2 Rgs2 Ucn3 0.638 1.506643227 0.276 0.284 0.01 Neuro-2 Ucn3 Wbp5 0.638 0.785474921 0.276 0.534 0.3 Neuro-2 Wbp5 Fam183b 0.631 0.942389731 0.262 0.307 0.044 Neuro-2 Fam183b Trpa1 0.628 1.153317961 0.256 0.261 0.005 Neuro-2 Trpa1 Gng12 0.625 0.910179636 0.25 0.386 0.158 Neuro-2 Gng12 Bex1 0.624 1.026203151 0.248 0.295 0.054 Neuro-2 Bex1 Akr1c14 0.618 1.189632011 0.236 0.273 0.042 Neuro-2 Akr1c14 Prnp 0.618 0.808232752 0.236 0.25 0.014 Neuro-2 Prnp Rasd1 0.615 1.017995093 0.23 0.261 0.035 Neuro-2 Rasd1 Ngfrap1 0.615 0.906830195 0.23 0.33 0.112 Neuro-2 Ngfrap1 Cpe 0.614 0.710599258 0.228 0.284 0.056 Neuro-2 Cpe 2810025M15Rik 0.613 0.968217482 0.226 0.307 0.086 Neuro-2 2810025M15Rik Glud1 0.613 0.799107704 0.226 0.409 0.217 Neuro-2 Glud1 S100a13 0.61 1.051760465 0.22 0.25 0.034 Neuro-2 S100a13 Pam 0.609 0.859083644 0.218 0.25 0.033 Neuro-2 Pam Qdpr 0.609 0.763429752 0.218 0.352 0.151 Neuro-2 Qdpr Cd81 0.609 0.481210094 0.218 0.602 0.456 Neuro-2 Cd81 Lmx1a 0.606 0.750313071 0.212 0.216 0.004 Neuro-2 Lmx1a Scn3a 0.604 0.937871535 0.208 0.216 0.009 Neuro-2 Scn3a Atf6 0.602 1.111947141 0.204 0.25 0.055 Neuro-2 Atf6 Atp6v0b 0.602 0.59668372 0.204 0.341 0.149 Neuro-2 Atp6v0b Neurod1 0.884 2.128413385 0.768 0.786 0.026 Neuro-1 Neurod1 Sct 0.847 2.612646934 0.694 0.75 0.075 Neuro-1 Sct Tuba1a 0.842 1.822329461 0.684 0.714 0.041 Neuro-1 Tuba1a Tm4sf4 0.825 1.651242079 0.65 0.75 0.125 Neuro-1 Tm4sf4 Chgb1 0.819 2.376568039 0.638 0.786 0.346 Neuro-1 Chgb Cpe1 0.806 2.243591797 0.612 0.643 0.057 Neuro-1 Cpe 5330417C22Rik 0.805 1.340264649 0.61 0.679 0.07 Neuro-1 5330417C22Rik Cystm11 0.793 0.885206025 0.586 0.929 0.632 Neuro-1 Cystm1 Cdkn1c 0.791 1.841786919 0.582 0.607 0.027 Neuro-1 Cdkn1c Plac8 0.788 1.189142517 0.576 0.893 0.568 Neuro-1 Plac8 Pcsk11 0.783 1.764650166 0.566 0.607 0.046 Neuro-1 Pcsk1 Scgn 0.78 2.035384076 0.56 0.571 0.018 Neuro-1 Scgn Sepp11 0.775 1.452403134 0.55 0.679 0.166 Neuro-1 Sepp1 Chga1 0.771 1.525323817 0.542 0.643 0.133 Neuro-1 Chga Fxyd3 0.771 1.366721839 0.542 0.714 0.244 Neuro-1 Fxyd3 Ptprn2 0.768 1.390558352 0.536 0.571 0.037 Neuro-1 Ptprn2 Fam183b1 0.766 1.652620862 0.532 0.571 0.047 Neuro-1 Fam183b Maged1 0.759 1.07059618 0.518 0.643 0.122 Neuro-1 Maged1 Oaz1 0.759 0.664384063 0.518 0.964 0.59 Neuro-1 Oaz1 Btg2 0.749 1.171651845 0.498 0.607 0.127 Neuro-1 Btg2 Eid1 0.743 1.191332762 0.486 0.536 0.053 Neuro-1 Eid1 Rfx6 0.74 1.593703157 0.48 0.5 0.02 Neuro-1 Rfx6 Gm609 0.734 1.188549643 0.468 0.5 0.031 Neuro-1 Gm609 Hmgcr 0.731 0.872682879 0.462 0.643 0.184 Neuro-1 Hmgcr Hist1h2bc 0.73 0.889355047 0.46 0.679 0.219 Neuro-1 Hist1h2bc Gfra3 0.727 1.473620087 0.454 0.464 0.01 Neuro-1 Gfra3 Olfm1 0.727 1.206923684 0.454 0.464 0.01 Neuro-1 Olfm1 Mien1 0.727 0.876810583 0.454 0.607 0.159 Neuro-1 Mien1 Cacna2d1 0.726 1.322721371 0.452 0.464 0.013 Neuro-1 Cacna2d1 Serpinb1a 0.725 1.255358649 0.45 0.643 0.224 Neuro-1 Serpinb1a Hepacam2 0.724 1.208501264 0.448 0.5 0.052 Neuro-1 Hepacam2 Cck 0.723 3.72352546 0.446 0.571 0.192 Neuro-1 Cck Krt7 0.723 0.983664388 0.446 0.643 0.224 Neuro-1 Krt7 Scg2 0.721 2.509476892 0.442 0.464 0.034 Neuro-1 Scg2 Ddc1 0.719 1.106062259 0.438 0.536 0.109 Neuro-1 Ddc Bnip3 0.718 1.06453224 0.436 0.607 0.194 Neuro-1 Bnip3 Hopx 0.718 0.73792621 0.436 0.679 0.235 Neuro-1 Hopx Pam1 0.717 1.443220648 0.434 0.464 0.035 Neuro-1 Pam Rab11a 0.714 0.727237716 0.428 0.607 0.169 Neuro-1 Rab11a St18 0.709 1.319288478 0.418 0.429 0.01 Neuro-1 St18 Syt13 0.709 1.136751386 0.418 0.429 0.011 Neuro-1 Syt13 Scg5 0.707 1.410374245 0.414 0.429 0.017 Neuro-1 Scg5 Insm1 0.706 1.20268774 0.412 0.429 0.014 Neuro-1 Insm1 Itm2c 0.706 1.091365278 0.412 0.5 0.089 Neuro-1 Itm2c Egr1 0.705 0.885933557 0.41 0.643 0.294 Neuro-1 Egr1 Slc25a4 0.703 0.931164692 0.406 0.571 0.174 Neuro-1 Slc25a4 Hmgn3 0.702 1.403371696 0.404 0.429 0.024 Neuro-1 Hmgn3 Sult1d1 0.702 0.923394046 0.404 0.571 0.193 Neuro-1 Sult1d1 Selm 0.701 1.058416696 0.402 0.536 0.144 Neuro-1 Selm Scp2 0.699 0.933147579 0.398 0.571 0.178 Neuro-1 Scp2 Prkar1a 0.699 0.754455307 0.398 0.607 0.202 Neuro-1 Prkar1a Junb 0.697 0.946778551 0.394 0.643 0.289 Neuro-1 Junb Lgals3bp 0.695 1.120877589 0.39 0.536 0.166 Neuro-1 Lgals3bp Ctsl1 0.694 0.932099684 0.388 0.464 0.077 Neuro-1 Ctsl Rev3l 0.693 0.843542085 0.386 0.464 0.077 Neuro-1 Rev3l Atp6v1b2 0.693 0.824876135 0.386 0.464 0.074 Neuro-1 Atp6v1b2 Cdkn1a 0.688 1.334292329 0.376 0.536 0.186 Neuro-1 Cdkn1a Cplx2 0.688 0.891165625 0.376 0.393 0.014 Neuro-1 Cplx2 Nae1 0.688 0.768573833 0.376 0.5 0.113 Neuro-1 Nae1 Peg3 0.686 1.681191988 0.372 0.393 0.021 Neuro-1 Peg3 Sis3 0.683 0.903960317 0.366 0.607 0.322 Neuro-1 Sis Ttr 0.682 0.97496334 0.364 0.464 0.108 Neuro-1 Ttr Plscr1 0.681 0.921872169 0.362 0.464 0.113 Neuro-1 Plscr1 Rap1a 0.68 0.65415806 0.36 0.5 0.126 Neuro-1 Rap1a Nefm 0.674 1.397081922 0.348 0.357 0.01 Neuro-1 Nefm Atp6v0d1 0.674 0.891032138 0.348 0.393 0.042 Neuro-1 Atp6v0d1 Ldlr 0.674 0.843862593 0.348 0.5 0.161 Neuro-1 Ldlr Gcc2 0.673 0.565358566 0.346 0.571 0.218 Neuro-1 Gcc2 Aplp1 0.671 1.274724387 0.342 0.357 0.015 Neuro-1 Aplp1 Myo6 0.671 0.862340558 0.342 0.571 0.247 Neuro-1 Myo6 Neurog3 0.669 1.358073317 0.338 0.357 0.021 Neuro-1 Neurog3 Ceacam10 0.669 1.0046749 0.338 0.357 0.017 Neuro-1 Ceacam10 Cdkn1b 0.668 0.788704545 0.336 0.464 0.13 Neuro-1 Cdkn1b Cst3 0.668 0.770195781 0.336 0.607 0.353 Neuro-1 Cst3 Dpp4 0.667 0.984749188 0.334 0.429 0.111 Neuro-1 Dpp4 Sdcbp 0.667 0.569776053 0.334 0.571 0.235 Neuro-1 Sdcbp Selk 0.666 0.736753309 0.332 0.5 0.168 Neuro-1 Selk Bsg 0.665 0.352410847 0.33 0.964 0.748 Neuro-1 Bsg Rbx1 0.664 0.649248485 0.328 0.607 0.288 Neuro-1 Rbx1 Nenf 0.663 1.011947665 0.326 0.393 0.076 Neuro-1 Nenf Fryl 0.663 0.852112737 0.326 0.393 0.068 Neuro-1 Fryl Cyp4b1 0.661 1.021061373 0.322 0.357 0.039 Neuro-1 Cyp4b1 Ube2b 0.66 0.646500382 0.32 0.536 0.233 Neuro-1 Ube2b Lamp2 0.659 0.728091995 0.318 0.464 0.142 Neuro-1 Lamp2 Dctn2 0.659 0.625768165 0.318 0.464 0.136 Neuro-1 Dctn2 Jun 0.659 0.498081031 0.318 0.786 0.456 Neuro-1 Jun Sh3bgrl 0.658 0.651226106 0.316 0.429 0.101 Neuro-1 Sh3bgrl H2-D1 0.658 0.468992101 0.316 0.643 0.29 Neuro-1 H2-D1 Reg42 0.342 0.627414828 0.316 0.071 0.388 Neuro-1 Reg4 Gadd45g 0.656 0.930147109 0.312 0.357 0.044 Neuro-1 Gadd45g Scg3 0.656 0.922207851 0.312 0.321 0.009 Neuro-1 Scg3 Smim6 0.656 0.755273791 0.312 0.393 0.074 Neuro-1 Smim6 Tecpr1 0.656 0.737106574 0.312 0.357 0.043 Neuro-1 Tecpr1 Marcks 0.656 0.562172873 0.312 0.536 0.218 Neuro-1 Marcks Aldoa 0.656 0.434817231 0.312 0.929 0.816 Neuro-1 Aldoa Isl1 0.655 1.111153862 0.31 0.321 0.012 Neuro-1 Isl1 Fev 0.655 1.046624972 0.31 0.321 0.011 Neuro-1 Fev Anxa6 0.655 1.024208104 0.31 0.321 0.01 Neuro-1 Anxa6 Acly 0.655 0.571220039 0.31 0.5 0.186 Neuro-1 Acly Ddx5 0.655 0.395316282 0.31 0.821 0.607 Neuro-1 Ddx5 Jak1 0.654 0.708996101 0.308 0.429 0.117 Neuro-1 Jak1 Map1b 0.653 0.999915565 0.306 0.321 0.014 Neuro-1 Map1b Hspa4l 0.653 0.91811242 0.306 0.357 0.053 Neuro-1 Hspa4l Prnp1 0.652 0.989747816 0.304 0.321 0.019 Neuro-1 Prnp Tspan1 0.652 0.590275966 0.304 0.5 0.198 Neuro-1 Tspan1 Os9 0.652 0.534705563 0.304 0.464 0.14 Neuro-1 Os9 Cyp51 0.651 0.483046862 0.302 0.607 0.28 Neuro-1 Cyp51 Upp1 0.65 1.068866358 0.3 0.321 0.021 Neuro-1 Upp1 Ids 0.65 0.826515129 0.3 0.321 0.02 Neuro-1 Ids Ndufa1 0.65 0.3916149 0.3 0.607 0.274 Neuro-1 Ndufa1 Qdpr1 0.649 0.626748098 0.298 0.464 0.155 Neuro-1 Qdpr Tspo 0.649 0.525363652 0.298 0.464 0.152 Neuro-1 Tspo Morf4l2 0.649 0.483584301 0.298 0.464 0.149 Neuro-1 Morf4l2 Mrfap1 0.649 0.398472237 0.298 0.607 0.293 Neuro-1 Mrfap1 Tac11 0.648 2.510656534 0.296 0.429 0.155 Neuro-1 Tac1 Ghrl 0.648 1.993849009 0.296 0.393 0.103 Neuro-1 Ghrl Fyttd1 0.647 0.611171171 0.294 0.429 0.128 Neuro-1 Fyttd1 Ubl3 0.647 0.557099795 0.294 0.429 0.124 Neuro-1 Ubl3 Eps8l2 0.647 0.528100525 0.294 0.429 0.12 Neuro-1 Eps8l2 Ginm1 0.646 1.043963068 0.292 0.357 0.069 Neuro-1 Ginm1 Gm15200 0.646 0.920483537 0.292 0.321 0.029 Neuro-1 Gm15200 Kif5b 0.646 0.661685371 0.292 0.643 0.349 Neuro-1 Kif5b Baiap2l2 0.646 0.594645445 0.292 0.464 0.16 Neuro-1 Baiap2l2 Copb1 0.645 0.60961529 0.29 0.464 0.173 Neuro-1 Copb1 Tusc3 0.645 0.609314836 0.29 0.357 0.061 Neuro-1 Tusc3 Tax1bp1 0.645 0.402266006 0.29 0.714 0.428 Neuro-1 Tax1bp1 Dst 0.644 0.905724655 0.288 0.321 0.032 Neuro-1 Dst Gadd45a 0.644 0.850106118 0.288 0.357 0.067 Neuro-1 Gadd45a Arrdc4 0.644 0.620840624 0.288 0.357 0.064 Neuro-1 Arrdc4 Arf1 0.644 0.482495611 0.288 0.571 0.301 Neuro-1 Arf1 Cd631 0.644 0.428425151 0.288 0.643 0.405 Neuro-1 Cd63 Hk2 0.643 0.879733309 0.286 0.393 0.109 Neuro-1 Hk2 Cldn4 0.643 0.809875647 0.286 0.393 0.113 Neuro-1 Cldn4 Dynlt3 0.643 0.480059235 0.286 0.429 0.128 Neuro-1 Dynlt3 Etv1 0.642 1.064894846 0.284 0.286 0.002 Neuro-1 Etv1 Gch1 0.642 1.0450736 0.284 0.321 0.04 Neuro-1 Gch1 Resp181 0.641 1.091625187 0.282 0.321 0.039 Neuro-1 Resp18 Emb 0.641 1.00297377 0.282 0.286 0.003 Neuro-1 Emb Ngfrap11 0.641 0.735608982 0.282 0.393 0.117 Neuro-1 Ngfrap1 Gucy2c 0.641 0.495671294 0.282 0.429 0.131 Neuro-1 Gucy2c Psmb4 0.641 0.451439702 0.282 0.643 0.346 Neuro-1 Psmb4 Insig1 0.641 0.363268224 0.282 0.464 0.151 Neuro-1 Insig1 Serinc1 0.64 0.710023389 0.28 0.357 0.076 Neuro-1 Serinc1 Actr3 0.64 0.483016253 0.28 0.607 0.313 Neuro-1 Actr3 Arl3 0.639 0.695992244 0.278 0.321 0.04 Neuro-1 Arl3 Txnip 0.639 0.626351931 0.278 0.571 0.317 Neuro-1 Txnip Ddx6 0.639 0.497496576 0.278 0.5 0.209 Neuro-1 Ddx6 Cdhr5 0.638 0.767618087 0.276 0.357 0.082 Neuro-1 Cdhr5 Dynlrb1 0.638 0.545490132 0.276 0.571 0.271 Neuro-1 Dynlrb1 Krt20 0.637 1.415109505 0.274 0.321 0.056 Neuro-1 Krt20 Pla2g2f 0.637 0.769734401 0.274 0.286 0.01 Neuro-1 Pla2g2f Brk1 0.637 0.637311984 0.274 0.5 0.225 Neuro-1 Brk1 Pkm 0.637 0.386573977 0.274 0.857 0.693 Neuro-1 Pkm H2-K1 0.637 0.386500238 0.274 0.714 0.458 Neuro-1 H2-K1 Ypel3 0.636 0.854256751 0.272 0.286 0.014 Neuro-1 Ypel3 Phip 0.634 0.678502118 0.268 0.393 0.124 Neuro-1 Phip Surf1 0.634 0.605793937 0.268 0.357 0.084 Neuro-1 Surf1 Tpm4 0.634 0.51443206 0.268 0.464 0.176 Neuro-1 Tpm4 Dnm2 0.634 0.419419665 0.268 0.393 0.109 Neuro-1 Dnm2 Rhob 0.633 0.721306707 0.266 0.321 0.052 Neuro-1 Rhob Ece1 0.633 0.615307723 0.266 0.321 0.052 Neuro-1 Ece1 Myl7 0.632 1.69538567 0.264 0.286 0.026 Neuro-1 Myl7 Idh3b 0.632 0.583175021 0.264 0.536 0.269 Neuro-1 Idh3b Slc35g1 0.631 0.670626441 0.262 0.357 0.089 Neuro-1 Slc35g1 Slc30a9 0.631 0.662004597 0.262 0.357 0.088 Neuro-1 Slc30a9 Mast2 0.631 0.538466203 0.262 0.321 0.052 Neuro-1 Mast2 Bex2 0.63 0.735198114 0.26 0.286 0.024 Neuro-1 Bex2 Itpr1 0.63 0.664400404 0.26 0.286 0.025 Neuro-1 Itpr1 Rab3c1 0.63 0.660261674 0.26 0.286 0.023 Neuro-1 Rab3c Selt 0.63 0.486789684 0.26 0.429 0.155 Neuro-1 Selt H3f3a 0.63 0.468318912 0.26 0.679 0.451 Neuro-1 H3f3a Tpst2 0.629 0.855541142 0.258 0.286 0.031 Neuro-1 Tpst2 Rab3d 0.629 0.834085966 0.258 0.321 0.062 Neuro-1 Rab3d Gipc2 0.629 0.418737057 0.258 0.5 0.212 Neuro-1 Gipc2 Prdx5 0.628 0.72018067 0.256 0.429 0.173 Neuro-1 Prdx5 Tmem126a 0.628 0.426597956 0.256 0.393 0.122 Neuro-1 Tmem126a Ugp2 0.628 0.417434372 0.256 0.429 0.158 Neuro-1 Ugp2 Vim1 0.627 1.339906798 0.254 0.286 0.033 Neuro-1 Vim Sec24d 0.627 0.755106003 0.254 0.286 0.03 Neuro-1 Sec24d Sqstm1 0.627 0.485067042 0.254 0.357 0.091 Neuro-1 Sqstm1 Arf5 0.626 0.592232353 0.252 0.464 0.216 Neuro-1 Arf5 Cyb5r3 0.625 0.606738759 0.25 0.393 0.149 Neuro-1 Cyb5r3 Vegfa 0.625 0.535171115 0.25 0.393 0.133 Neuro-1 Vegfa Sar1b 0.625 0.490212683 0.25 0.429 0.167 Neuro-1 Sar1b Cap1 0.625 0.383025912 0.25 0.393 0.125 Neuro-1 Cap1 Ubb 0.625 0.334489342 0.25 0.786 0.712 Neuro-1 Ubb Nefl 0.624 1.20990632 0.248 0.25 0.002 Neuro-1 Nefl Etnk1 0.624 0.649458229 0.248 0.321 0.071 Neuro-1 Etnk1 Eif4a2 0.624 0.523563686 0.248 0.5 0.252 Neuro-1 Eif4a2 Hsbp1 0.624 0.461879545 0.248 0.5 0.252 Neuro-1 Hsbp1 Laptm4a 0.624 0.441442055 0.248 0.536 0.281 Neuro-1 Laptm4a Mtch1 0.623 0.640341828 0.246 0.357 0.112 Neuro-1 Mtch1 Gng4 0.622 0.723471733 0.244 0.25 0.006 Neuro-1 Gng4 Rundc3a 0.622 0.713732891 0.244 0.25 0.006 Neuro-1 Rundc3a Dpysl2 0.622 0.704441597 0.244 0.321 0.075 Neuro-1 Dpysl2 Tm4sf5 0.622 0.61049843 0.244 0.536 0.335 Neuro-1 Tm4sf5 Efcab1 0.622 0.562908231 0.244 0.25 0.005 Neuro-1 Efcab1 Aamp 0.622 0.486727018 0.244 0.393 0.144 Neuro-1 Aamp Ier2 0.622 0.483283425 0.244 0.643 0.505 Neuro-1 Ier2 Smarce1 0.622 0.476584743 0.244 0.321 0.07 Neuro-1 Smarce1 Psma2 0.622 0.36892654 0.244 0.714 0.496 Neuro-1 Psma2 Rgs17 0.621 0.826822635 0.242 0.25 0.008 Neuro-1 Rgs17 Rab4a 0.621 0.628796173 0.242 0.286 0.041 Neuro-1 Rab4a Rnf214 0.621 0.533108865 0.242 0.286 0.041 Neuro-1 Rnf214 Ap3d1 0.621 0.509905514 0.242 0.357 0.109 Neuro-1 Ap3d1 Gcg 0.62 3.616153547 0.24 0.321 0.107 Neuro-1 Gcg Rprml 0.62 0.767657089 0.24 0.25 0.01 Neuro-1 Rprml Pim2 0.62 0.746028585 0.24 0.25 0.01 Neuro-1 Pim2 Oxr1 0.62 0.732104036 0.24 0.286 0.043 Neuro-1 Oxr1 Kif12 0.62 0.721616828 0.24 0.286 0.046 Neuro-1 Kif12 Celf3 0.62 0.511439169 0.24 0.25 0.008 Neuro-1 Celf3 Psap 0.619 0.578210901 0.238 0.393 0.152 Neuro-1 Psap Nktr 0.619 0.466699725 0.238 0.393 0.146 Neuro-1 Nktr Gnai2 0.619 0.453226523 0.238 0.393 0.145 Neuro-1 Gnai2 Rab2a 0.619 0.370444818 0.238 0.464 0.21 Neuro-1 Rab2a Tbrg1 0.619 0.335365008 0.238 0.429 0.161 Neuro-1 Tbrg1 4833439L19Rik 0.618 0.712557481 0.236 0.321 0.087 Neuro-1 4833439L19Rik Vps28 0.618 0.554298496 0.236 0.429 0.181 Neuro-1 Vps28 Hnrnph1 0.618 0.430451631 0.236 0.464 0.228 Neuro-1 Hnrnph1 Ostc 0.618 0.408836402 0.236 0.571 0.334 Neuro-1 Ostc Eif3a 0.618 0.287279795 0.236 0.679 0.435 Neuro-1 Eif3a Cacna1a 0.617 0.889867318 0.234 0.25 0.019 Neuro-1 Cacna1a Pdzd8 0.617 0.829682861 0.234 0.321 0.09 Neuro-1 Pdzd8 Gtf2a1 0.617 0.544648382 0.234 0.286 0.048 Neuro-1 Gtf2a1 Gnas 0.617 0.427487767 0.234 0.643 0.398 Neuro-1 Gnas Vasp 0.617 0.319618042 0.234 0.464 0.203 Neuro-1 Vasp Camk2n1 0.616 0.733682344 0.232 0.286 0.055 Neuro-1 Camk2n1 Slc25a11 0.616 0.63834965 0.232 0.357 0.127 Neuro-1 Slc25a11 Golim4 0.616 0.550686611 0.232 0.321 0.086 Neuro-1 Golim4 Gng121 0.616 0.495169993 0.232 0.393 0.163 Neuro-1 Gng12 Glud11 0.616 0.400650613 0.232 0.464 0.221 Neuro-1 Glud1 Sp3 0.616 0.320202491 0.232 0.321 0.078 Neuro-1 Sp3 Srrm2 0.616 0.294104548 0.232 0.714 0.457 Neuro-1 Srrm2 Ppp1r15a 0.615 0.763700584 0.23 0.286 0.058 Neuro-1 Ppp1r15a Sirt2 0.615 0.664318184 0.23 0.286 0.056 Neuro-1 Sirt2 Ppil4 0.615 0.552357747 0.23 0.321 0.085 Neuro-1 Ppil4 Minos1 0.615 0.413443932 0.23 0.714 0.519 Neuro-1 Minos1 Xiap 0.615 0.376258722 0.23 0.321 0.08 Neuro-1 Xiap Gabarap 0.615 0.352401663 0.23 0.607 0.354 Neuro-1 Gabarap Cnot4 0.614 0.752997617 0.228 0.321 0.09 Neuro-1 Cnot4 Wbp51 0.614 0.517147324 0.228 0.5 0.306 Neuro-1 Wbp5 Sfr1 0.614 0.458355534 0.228 0.393 0.161 Neuro-1 Sfr1 Azin1 0.614 0.431231125 0.228 0.393 0.153 Neuro-1 Azin1 Srp14 0.614 0.423130446 0.228 0.464 0.217 Neuro-1 Srp14 Tmem234 0.614 0.371723178 0.228 0.464 0.224 Neuro-1 Tmem234 Leprotl1 0.613 0.824622431 0.226 0.286 0.058 Neuro-1 Leprotl1 Atp6ap1 0.613 0.660330681 0.226 0.286 0.06 Neuro-1 Atp6ap1 Slc18a1 0.613 0.632640516 0.226 0.25 0.022 Neuro-1 Slc18a1 Tbc1d9 0.613 0.523268838 0.226 0.25 0.023 Neuro-1 Tbc1d9 Chmp5 0.613 0.422534415 0.226 0.393 0.157 Neuro-1 Chmp5 Canx 0.613 0.353930878 0.226 0.714 0.468 Neuro-1 Canx Cldn25 0.612 0.68249012 0.224 0.321 0.091 Neuro-1 Cldn25 Top1 0.612 0.511068369 0.224 0.5 0.266 Neuro-1 Top1 Ubn2 0.611 0.576308843 0.222 0.286 0.062 Neuro-1 Ubn2 Vamp3 0.611 0.505427761 0.222 0.321 0.094 Neuro-1 Vamp3 Fam216a 0.611 0.490493248 0.222 0.25 0.024 Neuro-1 Fam216a Cd24a2 0.61 0.746128857 0.22 0.607 0.512 Neuro-1 Cd24a Atf2 0.61 0.736043031 0.22 0.286 0.068 Neuro-1 Atf2 Tmem176b 0.61 0.595835674 0.22 0.393 0.162 Neuro-1 Tmem176b Adh11 0.61 0.498501311 0.22 0.464 0.245 Neuro-1 Adh1 Cxxc5 0.61 0.463738294 0.22 0.25 0.026 Neuro-1 Cxxc5 Atp1b3 0.61 0.40646453 0.22 0.321 0.093 Neuro-1 Atp1b3 Arpc5l 0.61 0.367536358 0.22 0.393 0.157 Neuro-1 Arpc5l Atp8b1 0.61 0.363695805 0.22 0.5 0.271 Neuro-1 Atp8b1 Uqcc2 0.61 0.252681284 0.22 0.607 0.378 Neuro-1 Uqcc2 Dusp4 0.609 0.836244373 0.218 0.25 0.034 Neuro-1 Dusp4 Anxa5 0.609 0.705362716 0.218 0.25 0.032 Neuro-1 Anxa5 Jhdm1d 0.609 0.645347078 0.218 0.25 0.032 Neuro-1 Jhdm1d Snap47 0.609 0.551184309 0.218 0.25 0.031 Neuro-1 Snap47 Clk1 0.609 0.510283388 0.218 0.429 0.209 Neuro-1 Clk1 Map1lc3b 0.609 0.45690213 0.218 0.357 0.133 Neuro-1 Map1lc3b Churc1 0.609 0.444224524 0.218 0.393 0.174 Neuro-1 Churc1 Ndufc1 0.609 0.408347599 0.218 0.714 0.486 Neuro-1 Ndufc1 Luc7l3 0.609 0.374051946 0.218 0.571 0.339 Neuro-1 Luc7l3 Tspan13 0.608 0.891546219 0.216 0.357 0.145 Neuro-1 Tspan13 Lcorl 0.608 0.841990473 0.216 0.286 0.074 Neuro-1 Lcorl Sema4a 0.608 0.747362665 0.216 0.286 0.072 Neuro-1 Sema4a Phldb2 0.608 0.739667636 0.216 0.25 0.035 Neuro-1 Phldb2 Rab15 0.608 0.647713069 0.216 0.25 0.033 Neuro-1 Rab15 Gpbp1l1 0.608 0.566865246 0.216 0.357 0.135 Neuro-1 Gpbp1l1 Acbd5 0.608 0.491092398 0.216 0.286 0.065 Neuro-1 Acbd5 Lcor 0.608 0.367222093 0.216 0.286 0.061 Neuro-1 Lcor Fabp5 0.607 1.225503564 0.214 0.286 0.082 Neuro-1 Fabp5 P4ha1 0.607 0.612242959 0.214 0.286 0.067 Neuro-1 P4ha1 H1f0 0.607 0.487676267 0.214 0.536 0.308 Neuro-1 H1f0 Nucb1 0.607 0.483110445 0.214 0.357 0.14 Neuro-1 Nucb1 Glyr1 0.607 0.476943139 0.214 0.357 0.142 Neuro-1 Glyr1 Azi2 0.607 0.427652555 0.214 0.357 0.136 Neuro-1 Azi2 Pycr2 0.607 0.384289142 0.214 0.286 0.063 Neuro-1 Pycr2 Sacm1l 0.607 0.326862348 0.214 0.286 0.061 Neuro-1 Sacm1l Fam105a 0.606 0.743129233 0.212 0.214 0.002 Neuro-1 Fam105a Mical2 0.606 0.689768591 0.212 0.25 0.039 Neuro-1 Mical2 Acadsb 0.606 0.669507803 0.212 0.25 0.037 Neuro-1 Acadsb Cnot6l 0.606 0.616579048 0.212 0.286 0.074 Neuro-1 Cnot6l Sh3glb1 0.606 0.594927841 0.212 0.357 0.157 Neuro-1 Sh3glb1 Smarcc2 0.606 0.502202951 0.212 0.321 0.108 Neuro-1 Smarcc2 Irf2bp2 0.606 0.373199108 0.212 0.429 0.206 Neuro-1 Irf2bp2 Pax6 0.605 0.827820437 0.21 0.214 0.004 Neuro-1 Pax6 Rasd11 0.605 0.793247153 0.21 0.25 0.041 Neuro-1 Rasd1 Rnf32 0.605 0.740146072 0.21 0.286 0.079 Neuro-1 Rnf32 Gnao1 0.605 0.71472288 0.21 0.214 0.004 Neuro-1 Gnao1 Man2a1 0.605 0.574074471 0.21 0.321 0.108 Neuro-1 Man2a1 Echdc2 0.605 0.509785118 0.21 0.286 0.069 Neuro-1 Echdc2 Znrf2 0.605 0.498279831 0.21 0.286 0.072 Neuro-1 Znrf2 D17Wsu104e 0.605 0.268534857 0.21 0.429 0.19 Neuro-1 D17Wsu104e Lect2 0.604 0.798940842 0.208 0.214 0.006 Neuro-1 Lect2 Disp2 0.604 0.723720707 0.208 0.214 0.006 Neuro-1 Disp2 Nudt4 0.604 0.616102524 0.208 0.286 0.08 Neuro-1 Nudt4 Clcn3 0.604 0.569540015 0.208 0.357 0.145 Neuro-1 Clcn3 Akr1c12 0.604 0.56406058 0.208 0.393 0.198 Neuro-1 Akr1c12 Kdelr2 0.604 0.529169196 0.208 0.464 0.288 Neuro-1 Kdelr2 Slc35b1 0.604 0.463153386 0.208 0.321 0.108 Neuro-1 Slc35b1 Rnf20 0.604 0.413882774 0.208 0.321 0.105 Neuro-1 Rnf20 0610011F06Rik 0.604 0.388542866 0.208 0.393 0.179 Neuro-1 0610011F06Rik Psmb5 0.604 0.273148038 0.208 0.464 0.23 Neuro-1 Psmb5 Cryba2 0.603 0.793991136 0.206 0.214 0.009 Neuro-1 Cryba2 Dgkd 0.603 0.736177799 0.206 0.286 0.084 Neuro-1 Dgkd Hmox2 0.603 0.685828848 0.206 0.286 0.082 Neuro-1 Hmox2 A1cf 0.603 0.636558699 0.206 0.25 0.045 Neuro-1 A1cf Tmem66 0.603 0.610368198 0.206 0.286 0.075 Neuro-1 Tmem66 Rap1b 0.603 0.604009718 0.206 0.286 0.082 Neuro-1 Rap1b Gnptg 0.603 0.51977512 0.206 0.25 0.042 Neuro-1 Gnptg Tuba4a 0.603 0.393541007 0.206 0.393 0.181 Neuro-1 Tuba4a Rpn1 0.603 0.35873066 0.206 0.536 0.303 Neuro-1 Rpn1 Vwa5b2 0.602 0.837552302 0.204 0.214 0.01 Neuro-1 Vwa5b2 Fgd2 0.602 0.692969634 0.204 0.214 0.01 Neuro-1 Fgd2 Glul 0.602 0.597853242 0.204 0.286 0.085 Neuro-1 Glul Ppap2a 0.602 0.542704762 0.204 0.25 0.044 Neuro-1 Ppap2a Impa1 0.602 0.526924865 0.204 0.321 0.121 Neuro-1 Impa1 Rhoa 0.602 0.452337591 0.204 0.464 0.258 Neuro-1 Rhoa Emc7 0.602 0.374283991 0.204 0.321 0.107 Neuro-1 Emc7 Fos 0.602 0.366765775 0.204 0.607 0.409 Neuro-1 Fos Ppp4c 0.602 0.344513394 0.204 0.429 0.21 Neuro-1 Ppp4c Ssu72 0.602 0.280576353 0.204 0.464 0.225 Neuro-1 Ssu72 2810025M15Rik1 0.601 0.806213089 0.202 0.286 0.092 Neuro-1 2810025M15Rik Tle6 0.601 0.612081752 0.202 0.214 0.011 Neuro-1 Tle6 Nrp1 0.601 0.583612063 0.202 0.214 0.011 Neuro-1 Nrp1 Pdhb 0.601 0.545941142 0.202 0.357 0.136 Neuro-1 Pdhb Slu7 0.601 0.445622881 0.202 0.286 0.078 Neuro-1 Slu7 Rrp1 0.601 0.437041314 0.202 0.429 0.228 Neuro-1 Rrp1 Sdf4 0.601 0.363891924 0.202 0.357 0.145 Neuro-1 Sdf4 Papss1 0.601 0.352345333 0.202 0.286 0.074 Neuro-1 Papss1 Papola 0.601 0.334457209 0.202 0.464 0.232 Neuro-1 Papola Bdp1 0.601 0.306372422 0.202 0.321 0.106 Neuro-1 Bdp1 Arpc5 0.601 0.297752962 0.202 0.464 0.249 Neuro-1 Arpc5 Table 1C. InVivo Cluster 11 (Paneth Cells) vs Top 200 ENR-4 cells (FIG. 1G InVivo vs ENR) Gene p_val avg_diff pct.1 pct.2 Defa22 4.37E−141 2.971300119 1 0.625 Defa21 4.13E−135 2.928723434 1 0.765 Fabp6 3.29E−71 2.794414465 0.799 0 Apoa1 5.19E−41 2.167526278 0.735 0.125 Defa20 3.41E−48 2.136944081 0.635 0.005 Gm26924 9.46E−139 2.121543914 1 0.915 Gm15564 2.05E−61 2.024788068 0.878 0.135 Zg16 6.80E−23 1.974431612 0.471 0.045 Mptx2 1.38E−45 1.946653592 0.788 0.095 Reg3b 1.46E−29 1.895225306 0.561 0.055 Gm15292 4.85E−66 1.843395367 0.952 0.37 Reg3g 7.87E−34 1.734499905 0.608 0.07 Defa26 1.30E−81 1.67834991 0.995 0.855 Defa5 6.75E−34 1.665483508 0.698 0.13 Clec2h 5.66E−38 1.665239259 0.545 0.01 Chd8 6.88E−16 1.658113819 0.36 0.04 mmu-mir-6236 1.22E−42 1.641473397 0.587 0.005 Lyz1 4.54E−77 1.581447916 1 0.93 Fabp2 8.63E−37 1.546973338 0.942 0.625 Pnliprp2 5.32E−41 1.520921921 0.878 0.32 Defa-rs7 3.06E−38 1.513071859 0.841 0.43 Defa2 3.22E−37 1.503489671 0.508 0 Ang4 3.92E−75 1.496055114 1 0.765 Gm21002 2.36E−33 1.443051807 0.466 0 Gm15293 2.15E−38 1.41558284 0.852 0.23 Spink3 3.43E−25 1.412229842 0.481 0.04 Sepp1 5.17E−20 1.367808281 0.524 0.12 Anpep 2.20E−26 1.322268451 0.524 0.05 Gm10104 1.62E−42 1.264917901 0.979 0.63 Crip1 1.59E−31 1.157051096 0.894 0.45 Lbh 2.73E−22 1.145440013 0.487 0.06 Gm15308 2.36E−33 1.12386933 0.466 0 Lars2 8.64E−33 1.09806747 0.91 0.56 Ccl6 6.02E−31 1.024182325 0.905 0.385 Mptx1 4.76E−12 0.992620758 0.413 0.095 Slc51a 2.21E−16 0.984051209 0.28 0.005 Bambi 7.58E−17 0.977064848 0.37 0.04 Krt20 1.39E−16 0.972788693 0.36 0.04 Clca3 2.99E−10 0.967743346 0.19 0.015 Defa3 2.92E−37 0.952791523 0.989 0.835 Gm15315 2.21E−26 0.943824914 0.974 0.65 Hpgd 7.14E−18 0.879485606 0.439 0.065 Lyz2 1.21E−19 0.849112831 0.804 0.345 Plb1 3.74E−13 0.787790121 0.206 0 Atf3 7.30E−10 0.767720706 0.444 0.155 Fos 3.10E−14 0.760694898 0.788 0.42 Nupr1 9.01E−14 0.75178466 0.741 0.365 Apoa4 1.54E−07 0.744899359 0.286 0.075 St3gal4 2.78E−11 0.744187874 0.317 0.07 Gm7849 2.39E−11 0.737872833 0.386 0.095 Slc6a19 6.56E−12 0.73638031 0.169 0.01 Naaladl1 1.42E−11 0.727332221 0.212 0.005 Guca2b 1.29E−16 0.708643403 0.804 0.385 Pepd 4.24E−08 0.701308814 0.228 0.04 Muc3 1.02E−11 0.689025992 0.185 0 Ace2 2.99E−10 0.6808095 0.233 0.03 Dpep1 1.28E−09 0.666476273 0.153 0 Sgk1 2.33E−15 0.654045271 0.238 0 Tram1 5.74E−13 0.651849688 0.54 0.2 Enpep 5.00E−10 0.65108564 0.19 0.01 Nucb2 4.31E−12 0.650267512 0.386 0.08 Slc15a1 6.19E−09 0.643708175 0.143 0 Reg4 6.58E−13 0.638836262 0.899 0.695 Cndp2 2.65E−08 0.629322791 0.238 0.035 Trp53inp1 1.08E−13 0.620023867 0.249 0.015 Habp2 6.60E−11 0.612716764 0.402 0.105 AY761185 7.79E−13 0.605913705 0.974 0.91 2010106E10Rik 2.82E−09 0.604128191 0.148 0 Mep1b 4.15E−07 0.602377603 0.206 0.03 Ggh 6.28E−14 0.595102485 0.392 0.08 Maf 6.42E−08 0.592753887 0.127 0 2200002D01Rik 1.12E−05 0.591231351 0.481 0.27 Qsox1 5.34E−10 0.588808803 0.455 0.15 Lct 1.26E−05 0.57120206 0.138 0.015 Fosb 6.76E−11 0.560028909 0.323 0.065 Ace 6.42E−08 0.554965613 0.127 0 Tmigd1 6.19E−09 0.55155353 0.143 0 Ccl5 1.39E−07 0.544612494 0.122 0 Cyp4f14 3.06E−07 0.526821249 0.233 0.045 Slc27a4 9.26E−05 0.517682324 0.169 0.035 Agpat2 3.38E−07 0.516384527 0.175 0.02 Slc9a3r1 5.69E−07 0.513423379 0.27 0.075 Snord13 8.67E−08 0.510552511 0.402 0.15 Muc2 1.39E−11 0.509630225 0.661 0.305 Gm10936 1.97E−12 0.509271194 0.196 0 Slc5a1 6.57E−08 0.50910138 0.36 0.115 Sult1d1 2.87E−12 0.50864725 0.36 0.1 Aoc1 4.26E−05 0.506515765 0.222 0.06 Ggt1 5.66E−08 0.50249154 0.159 0.02 Maoa 7.11E−06 0.502189218 0.302 0.105 Mpp1 2.26E−06 0.499008165 0.148 0.015 Specc1l 3.33E−06 0.489499836 0.196 0.035 Acox1 2.64E−09 0.487666729 0.201 0.04 P4hb 2.80E−10 0.486750375 0.889 0.71 Apob 0.002443035 0.485889273 0.206 0.08 Serpinb1a 2.36E−05 0.485316763 0.37 0.155 Herpud1 1.64E−11 0.482518432 0.487 0.175 Smim22 0.000134645 0.480130631 0.27 0.1 n-R5-8s1 5.18E−11 0.477213392 0.175 0 Tmem59 1.72E−10 0.474309308 0.54 0.225 Smim14 4.75E−12 0.471404187 0.508 0.185 Sel1l 9.55E−10 0.46843993 0.339 0.09 Cd74 2.91E−06 0.467581391 0.101 0 Mmp7 8.54E−12 0.462845043 0.958 0.78 Dnajc3 3.31E−08 0.459761476 0.529 0.24 Agt 1.53E−07 0.453836347 0.185 0.025 Gm14850 2.84E−06 0.453763771 0.794 0.565 Slc51b 1.91E−06 0.453513929 0.127 0.005 Tmem120a 3.51E−07 0.45153161 0.127 0.01 Rpl41 4.20E−10 0.450732693 0.825 0.71 Gm1123 2.93E−09 0.448735633 0.73 0.415 Cdh17 2.98E−08 0.447834443 0.471 0.21 Dgat1 7.71E−09 0.447274671 0.259 0.065 Apoc3 0.000902415 0.441130264 0.18 0.055 Xpnpep2 0.001543925 0.439544921 0.106 0.02 Egr1 4.63E−06 0.428981363 0.524 0.3 Dnajb1 5.76E−05 0.423553841 0.132 0.015 Prr15 3.91E−10 0.422498409 0.392 0.125 Tob1 2.30E−08 0.421001312 0.328 0.1 Rfk 4.62E−06 0.419983828 0.36 0.15 Cap1 7.01E−05 0.414248403 0.19 0.055 Gdpd1 1.85E−06 0.406359879 0.302 0.1 Mep1a 3.50E−07 0.405859626 0.138 0.005 Klf6 3.56E−07 0.405271351 0.349 0.135 H2-Q2 0.000259328 0.404634689 0.175 0.045 Amn 3.35E−05 0.404149314 0.138 0.025 Galnt3 0.000191936 0.403926453 0.185 0.05 Ell2 1.30E−08 0.40366623 0.254 0.05 Car4 2.91E−06 0.403314629 0.101 0 Hsd17b11 0.002400711 0.402198995 0.153 0.055 Muc13 1.30E−07 0.401509767 0.651 0.38 Lamp1 1.96E−09 0.401141149 0.46 0.195 Tspan1 1.41E−07 0.400356554 0.582 0.295 Pim3 2.72E−09 0.39587135 0.286 0.065 Mcfd2 9.13E−07 0.392218274 0.27 0.075 Gfpt1 3.45E−07 0.387017679 0.434 0.195 Uba5 2.36E−12 0.385892816 0.265 0.04 Mgat4c 2.91E−06 0.381944744 0.101 0 Dap 1.11E−09 0.375080268 0.312 0.085 Ahnak 0.000128755 0.374612673 0.106 0.025 Xpnpep1 7.27E−06 0.374399986 0.206 0.05 Slc30a2 9.59E−11 0.373579233 0.201 0.015 Tapbp 0.011259039 0.367549589 0.138 0.045 Vil1 1.34E−05 0.366379599 0.45 0.235 Arf6 6.40E−06 0.363901601 0.265 0.085 Ano6 2.26E−06 0.362532519 0.19 0.04 Ifngr2 8.01E−06 0.358845113 0.201 0.045 Cobl 5.71E−05 0.356541596 0.18 0.04 Galnt5 1.93E−06 0.351590655 0.169 0.025 Creb3l3 0.000415311 0.350252677 0.111 0.02 Dio1 2.65E−10 0.350121362 0.175 0.005 Naip5 0.000142433 0.348866348 0.106 0.01 Sult2b1 0.000270839 0.348098073 0.101 0.015 Sox9 7.43E−06 0.344985408 0.333 0.13 Mlx 4.37E−05 0.344789164 0.18 0.04 Tmem54 0.000506993 0.344438204 0.18 0.05 Mgam 0.000123288 0.343745106 0.402 0.215 Btg2 0.000121852 0.341475665 0.312 0.135 Smpdl3a 4.57E−08 0.341385732 0.175 0.03 Lman1 5.05E−09 0.33990403 0.397 0.175 Jun 0.000267656 0.338610563 0.672 0.49 Mia3 1.69E−06 0.335872209 0.302 0.11 Surf4 3.77E−08 0.333373357 0.402 0.16 Cdhr2 0.000143206 0.333323199 0.217 0.07 Chka 0.038995206 0.333035923 0.127 0.05 Itm2c 3.77E−06 0.326377206 0.196 0.04 Abhd2 3.70E−05 0.326335546 0.201 0.06 Gorasp2 2.51E−05 0.325246575 0.201 0.065 Pdxdc1 2.12E−06 0.325063024 0.275 0.11 Psmb10 2.49E−05 0.324199131 0.243 0.09 Gm24601 2.82E−09 0.323704332 0.148 0 Uggt1 0.000114071 0.32358108 0.196 0.055 Iqgap2 0.000868689 0.322731261 0.116 0.02 Mogat2 0.003938893 0.322648461 0.106 0.02 Fahd1 0.000260504 0.322487688 0.148 0.035 Slc43a2 8.66E−08 0.322337795 0.143 0.01 Rnf128 4.69E−09 0.321252309 0.503 0.235 Slc35b1 0.000272326 0.319967392 0.302 0.14 Ube2q1 7.73E−05 0.319246074 0.111 0.02 Id3 0.001645875 0.318742649 0.169 0.07 Gna11 0.003336519 0.317578908 0.201 0.08 Ms4a8a 0.006912337 0.316318026 0.143 0.05 Cdx1 2.57E−06 0.312896649 0.354 0.155 Asph 5.44E−08 0.311566443 0.386 0.155 Sis 0.001703562 0.310173334 0.439 0.265 Atg7 0.00413282 0.308839601 0.132 0.04 Prpsap1 0.043738471 0.307741514 0.148 0.07 Gucy2c 4.20E−06 0.307721748 0.212 0.06 Klf4 0.000604214 0.30710746 0.233 0.095 Ilvbl 0.000887904 0.304942158 0.111 0.02 Ubl3 9.61E−07 0.303993675 0.302 0.11 Aqp1 9.45E−05 0.30070659 0.291 0.13 Sppl2a 1.40E−09 0.300006334 0.36 0.125 Il17rc 0.001566829 0.298723577 0.106 0.02 Itm2b 3.19E−08 0.295962793 0.571 0.33 Faah 0.012089429 0.295046927 0.111 0.03 Creld2 0.001229486 0.294560522 0.169 0.06 Ndfip1 7.03E−07 0.291913484 0.175 0.03 Osbpl2 5.11E−05 0.291474585 0.143 0.025 Krt19 0.000106004 0.288785016 0.63 0.475 Ces2e 0.000691047 0.288567477 0.27 0.15 Edem1 5.75E−08 0.288168169 0.243 0.06 Slc13a1 0.000142059 0.286560678 0.101 0.005 Nucb1 5.67E−08 0.286046342 0.323 0.14 Alpi 0.000522112 0.285914771 0.101 0.02 Arfgap3 2.29E−07 0.284604745 0.328 0.135 Ghr 7.96E−07 0.282348463 0.111 0.015 Ckmt1 0.003470725 0.282030097 0.296 0.15 Galnt4 1.13E−05 0.279673278 0.185 0.04 Erlin2 7.55E−07 0.279047894 0.127 0.015 Erp44 5.53E−06 0.278446677 0.265 0.1 Tulp4 3.17E−08 0.277590145 0.243 0.07 Nlrc4 8.78E−05 0.277361037 0.159 0.04 Defa25 0.000529513 0.276550267 0.185 0.06 Samd5 1.46E−07 0.276534496 0.143 0.005 Mttp 0.002099111 0.276373894 0.18 0.09 Tm9sf3 1.69E−05 0.276308422 0.614 0.41 Pllp 2.46E−06 0.276273409 0.159 0.02 Tmprss2 9.22E−11 0.274430929 0.439 0.185 Cox7a1 0.000591463 0.272661291 0.106 0.025 Me2 0.001469951 0.272428052 0.254 0.12 Slc41a1 1.32E−05 0.272322566 0.116 0.005 Sult1b1 0.052418679 0.272261175 0.153 0.07 Zzef1 0.04064896 0.271587691 0.101 0.03 Zcchc6 0.005104942 0.27126706 0.143 0.045 Pls1 1.18E−05 0.271040751 0.312 0.165 Wnt3 1.91E−06 0.270361588 0.217 0.065 Dpp4 0.013324936 0.269524372 0.175 0.08 Spop 6.48E−05 0.268255044 0.243 0.09 Mtus1 5.54E−05 0.268190034 0.159 0.035 Rsrc2 3.03E−05 0.26619444 0.212 0.065 Lsm2 0.011241648 0.266112529 0.111 0.045 Tm9sf2 2.80E−06 0.26578344 0.333 0.15 Cast 1.67E−06 0.265356048 0.19 0.045 Serpinb6a 2.25E−05 0.265321679 0.349 0.17 B2m 1.22E−07 0.265294692 0.624 0.37 Usp4 0.047805332 0.264431871 0.122 0.055 Chpt1 0.00051801 0.263791385 0.122 0.03 Lasp1 0.002783276 0.261137016 0.175 0.065 0610007N19Rik 4.63E−05 0.260238033 0.254 0.095 Bex1 0.000128886 0.258681196 0.217 0.075 Tsc22d3 0.000742124 0.258389596 0.106 0.015 Becn1 0.019633687 0.258366841 0.138 0.075 Rab11fip1 0.000104016 0.257750496 0.175 0.05 Coro2a 0.069057442 0.257080355 0.138 0.06 Epb4.1l3 0.102862223 0.256648972 0.138 0.065 Sord 1.84E−05 0.256495779 0.365 0.175 Mgat4a 1.70E−07 0.256129885 0.175 0.05 Jup 0.000332364 0.255734102 0.159 0.06 Itch 0.000553636 0.255632 0.159 0.045 Adipor2 0.000133973 0.255453283 0.249 0.1 Aftph 0.000228287 0.254680924 0.143 0.03 Pdcd4 0.000306405 0.254674262 0.312 0.16 Golph3 0.000415686 0.253598707 0.148 0.04 Chdh 0.00055323 0.25303635 0.111 0.02 Erbb2ip 2.04E−05 0.253005599 0.212 0.065 Hspa5 1.23E−06 0.252047696 0.841 0.595 Fam174b 3.11E−07 0.251850066 0.222 0.06 Azin1 5.36E−08 0.25153542 0.228 0.07 Ufl1 0.002157661 0.251488874 0.164 0.06 Ndufa3 9.12E−05 0.251323466 0.392 0.225 Cdhr5 8.38E−06 0.251201316 0.307 0.145 Rpl27 0.127703322 −0.255954126 0.058 0.12 Trappc1 0.0057506 −0.25942388 0.053 0.105 Coro1b 0.048898712 −0.260140134 0.111 0.165 Rtn3 1.62E−09 −0.263284381 0.249 0.18 Xpot 0.08381105 −0.263596897 0.053 0.105 Ptp4a2 1.67E−08 −0.264228486 0.349 0.265 Kcnq1 0.161443028 −0.272560147 0.085 0.14 Rpl34 3.84E−07 −0.2732009 0.667 0.73 Psmb7 0.063524749 −0.280529908 0.037 0.105 Kif5b 6.88E−09 −0.281414188 0.386 0.295 Smarcb1 0.014359485 −0.289993549 0.042 0.12 Marcks 0.037513635 −0.293336842 0.079 0.13 Fau 0.041224122 −0.293696089 0.159 0.22 Mlf2 0.012682846 −0.297165151 0.132 0.185 Gm7589 0.010202787 −0.297802749 0.053 0.115 Ppp1r14d 0.002510985 −0.301894835 0.138 0.19 Srebf2 0.008271236 −0.310036738 0.048 0.11 Mpdu1 0.000543468 −0.313369273 0.058 0.115 Dpy30 0.006589504 −0.313641409 0.122 0.185 Slc29a1 0.000912654 −0.318739334 0.048 0.11 Nono 0.012584766 −0.319001563 0.079 0.16 Dbnl 0.014534277 −0.3229847 0.053 0.12 Tagln2 0.000294237 −0.325409509 0.238 0.295 Esrp1 0.016142497 −0.331057179 0.074 0.125 Car9 0.004265633 −0.331187058 0.063 0.125 Drg1 0.023481733 −0.332309493 0.074 0.14 Spr 0.012739204 −0.333206136 0.074 0.135 Rsbn1l 0.036794841 −0.339510977 0.058 0.11 Dars 0.002015536 −0.339945586 0.095 0.16 Sin3b 0.010991341 −0.340271235 0.069 0.135 Gm15299 0.000939182 −0.341600428 0.873 0.93 Ndufa12 0.006525634 −0.342054107 0.222 0.29 Huwe1 0.001734803 −0.342766858 0.122 0.175 Ldlr 0.001764872 −0.343292498 0.101 0.155 1500011K16Rik 0.082359853 −0.347961666 0.095 0.175 Reep6 0.037455675 −0.348190857 0.069 0.135 Sdc1 0.018810094 −0.350542057 0.042 0.115 Adh5 0.003478901 −0.351308036 0.127 0.185 Krcc1 0.00084717 −0.355527421 0.148 0.21 Ndufab1 0.000336451 −0.355935419 0.212 0.275 Myl12a 0.003503618 −0.356203714 0.233 0.285 Mtx2 0.002650821 −0.357088917 0.079 0.13 Ddx39 0.004509039 −0.359706067 0.048 0.125 Siva1 0.001396691 −0.360067427 0.074 0.125 Cnih1 0.002652698 −0.361640512 0.069 0.135 Ptpla 0.003697567 −0.361645865 0.069 0.155 Csrp2 0.001939061 −0.362818073 0.169 0.22 Phf5a 0.000298916 −0.365855881 0.095 0.15 Rnaset2b 0.000421673 −0.366072338 0.053 0.11 Cmc1 0.009540242 −0.367479096 0.058 0.135 Bzw2 0.006296271 −0.368043119 0.085 0.145 Cct8 0.013411026 −0.368975722 0.169 0.225 Hspd1 5.60E−06 −0.36940695 0.349 0.435 Sec61g 0.001204529 −0.369587077 0.058 0.12 Mlxipl 0.003207373 −0.369662267 0.074 0.135 Smc2 0.011280986 −0.370477194 0.069 0.12 Rps18-ps3 0.010664087 −0.370689313 0.079 0.16 Hk2 0.001735551 −0.371079347 0.042 0.115 Rrs1 0.012692596 −0.371114753 0.048 0.11 Lsm3 0.003177197 −0.372083598 0.069 0.14 Slc25a4 0.019197025 −0.373137077 0.037 0.12 Ndufs7 1.17E−06 −0.37455708 0.238 0.3 Atad2 0.021168596 −0.374980489 0.037 0.105 Sqle 0.021315342 −0.37548791 0.085 0.155 Nfib 0.000862975 −0.376946487 0.048 0.115 Hist1h1e 0.012839513 −0.377323631 0.122 0.22 Trappc6a 0.001874064 −0.377461527 0.095 0.18 Gm4204 0.002031844 −0.37823936 0.026 0.115 Cct3 0.000292286 −0.37919542 0.18 0.24 Cyr61 0.000709331 −0.379718957 0.063 0.12 Bbip1 0.024183248 −0.380138122 0.101 0.16 Smim11 0.00081875 −0.380275098 0.063 0.125 Rbm3 0.003354399 −0.380533039 0.063 0.12 Pnn 0.001375366 −0.380929729 0.101 0.175 Cyc1 1.76E−06 −0.381028444 0.259 0.355 Lsm5 0.014353946 −0.381788077 0.026 0.105 Dtymk 0.003462617 −0.382914926 0.159 0.23 Gpx4 0.001236908 −0.385447789 0.085 0.17 Prmt1 0.005873983 −0.38737595 0.106 0.18 Akr1c13 0.000615651 −0.388385966 0.143 0.21 Phpt1 0.001175685 −0.38875707 0.058 0.135 Zfp292 0.006069326 −0.389741258 0.153 0.21 Gm3940 0.003149773 −0.390000209 0.021 0.105 Ugdh 0.00203156 −0.390862375 0.111 0.17 Cox8a 6.81E−07 −0.392352404 0.587 0.645 Sdhb 0.003482545 −0.394556643 0.233 0.335 S100a6 0.000126973 −0.394972675 0.101 0.155 Cct4 0.000124021 −0.396040082 0.222 0.295 Rpl31 0.009329667 −0.396617136 0.106 0.195 Hint1 1.28E−05 −0.396735031 0.635 0.71 Ccdc59 0.000483844 −0.398492584 0.053 0.12 Lss 0.000507684 −0.399008959 0.021 0.105 Rps26-ps1 0.000324404 −0.399038177 0.132 0.185 Snrpd2 0.000284499 −0.399355159 0.201 0.29 Eef1e1 6.43E−05 −0.399521435 0.069 0.125 Gcat 0.010409293 −0.400031144 0.058 0.12 Rbbp7 0.000173531 −0.400052877 0.138 0.205 Esf1 0.001968666 −0.400652886 0.074 0.13 Dnajc15 0.001562907 −0.401490758 0.079 0.15 U2surp 0.001546117 −0.402009386 0.111 0.175 Aqp4 0.000123984 −0.402019345 0.053 0.125 Cyb5b 0.000128385 −0.402989636 0.18 0.235 Cpox 0.000314131 −0.403859864 0.037 0.105 Tmem97 0.000129303 −0.403971676 0.069 0.205 Polr2e 0.000723205 −0.404438373 0.116 0.195 Lyar 0.000849363 −0.405128888 0.085 0.145 Gsta1 0.008488495 −0.406214333 0.058 0.115 Hist1h1b 0.015463707 −0.409282642 0.053 0.14 Ppp1r11 0.00076078 −0.409341331 0.074 0.15 Mrpl20 0.000222405 −0.4097286 0.169 0.225 Prap1 0.000322123 −0.410147265 0.317 0.39 Fus 0.001200168 −0.410755506 0.153 0.225 Galk1 0.000966106 −0.411001986 0.042 0.14 Actr3 0.000472547 −0.411992211 0.243 0.325 Shfm1 1.16E−06 −0.412270568 0.429 0.5 Anp32b 5.33E−05 −0.412314848 0.249 0.32 Dnajc2 0.006981482 −0.413764325 0.122 0.2 Ddx39b 2.31E−05 −0.414727855 0.169 0.23 Ktn1 0.000858275 −0.414734759 0.132 0.195 Gm1840 6.64E−05 −0.414910439 0.016 0.115 Dynlt1a 0.00069428 −0.415288469 0.021 0.12 Mrps26 0.000178848 −0.416003885 0.063 0.145 Fubp1 0.001359574 −0.416020211 0.138 0.205 Chchd1 0.010693856 −0.416079298 0.122 0.19 H2afx 0.008029842 −0.417628727 0.058 0.135 Mrpl40 0.007616431 −0.418501576 0.101 0.155 Oard1 0.000339221 −0.418575087 0.063 0.13 Tbca 0.000688725 −0.419134115 0.159 0.21 Taf9 7.14E−06 −0.420752889 0.111 0.17 Gsto1 0.001802233 −0.420965768 0.296 0.37 Gsta4 0.003632296 −0.421782008 0.048 0.12 Park7 0.001832937 −0.422425482 0.254 0.33 Sssca1 0.000453976 −0.424845578 0.032 0.105 Esco2 0.003298742 −0.42524584 0.026 0.11 Cdca8 0.015823827 −0.425969757 0.058 0.145 Pak1ip1 0.001678301 −0.426570744 0.069 0.14 Nop56 4.45E−05 −0.427123551 0.143 0.195 Eif3e 7.20E−05 −0.427342463 0.212 0.265 Tmem261 0.002187429 −0.428519281 0.095 0.17 Slc1a5 2.46E−06 −0.4287541 0.153 0.205 2410006H16Rik 9.53E−06 −0.429497157 0.471 0.55 Lgals2 3.38E−16 −0.43136214 0.862 0.935 Tpm4 0.000105125 −0.431476714 0.111 0.19 Pa2g4 1.84E−06 −0.432182506 0.344 0.395 Pafah1b3 0.001454846 −0.433493801 0.138 0.21 Tnfrsf12a 0.00128252 −0.433556527 0.026 0.105 Ndufa4 1.30E−06 −0.433746388 0.64 0.71 Nudcd2 0.00058607 −0.436797764 0.085 0.145 Glrx3 0.000274264 −0.436973196 0.153 0.22 Alad 0.002003834 −0.437174302 0.063 0.14 Hsd17b13 0.001039365 −0.437323307 0.026 0.13 Cnn3 8.87E−05 −0.437469591 0.085 0.15 Mrps28 0.000527309 −0.437536599 0.074 0.15 Hspa4 0.000168537 −0.437692081 0.196 0.265 Gm10073 0.004118379 −0.437808073 0.063 0.165 Iah1 0.001130548 −0.438405123 0.058 0.135 Psmb1 1.61E−05 −0.43864532 0.402 0.46 Gnl3 1.56E−05 −0.438657513 0.148 0.205 Rpl36-ps3 0.000953701 −0.439253378 0.058 0.16 Josd2 0.001224583 −0.439700566 0.037 0.105 Esd 4.64E−05 −0.440843374 0.243 0.33 0610009B22Rik 2.00E−06 −0.443812702 0.042 0.115 Gm17430 6.18E−05 −0.443838706 0.063 0.125 Trim27 0.00016397 −0.44496242 0.048 0.125 Smoc2 0.001514418 −0.4451081 0.238 0.32 Sepw1 0.000502909 −0.445526261 0.132 0.195 Mrpl12 1.09E−07 −0.445549068 0.254 0.325 Pfkp 0.000561123 −0.446513952 0.058 0.14 Nasp 0.012646494 −0.446850026 0.063 0.145 Ndufa2 1.42E−09 −0.447289951 0.36 0.435 Set 3.66E−06 −0.448964645 0.169 0.29 Polr3k 0.005121693 −0.449065307 0.079 0.16 Eif3i 6.32E−08 −0.449706207 0.291 0.395 Mrpl28 0.000553959 −0.450265998 0.143 0.215 Polr2g 2.63E−05 −0.452332415 0.063 0.135 Atf5 1.08E−06 −0.452393729 0 0.11 Slc25a39 0.00010006 −0.453722911 0.138 0.205 Rpl39 2.49E−13 −0.453761377 0.741 0.8 Commd3 0.000307934 −0.454288259 0.101 0.165 Mrps10 0.002572342 −0.455359878 0.021 0.11 Dazap1 3.16E−05 −0.455370577 0.074 0.16 Tstd1 0.001212988 −0.455430685 0.106 0.175 Ahcy 3.72E−05 −0.45666475 0.122 0.205 Cox7a2l 1.48E−05 −0.456700532 0.27 0.38 1190007I07Rik 0.000250159 −0.456781329 0.058 0.145 Hspa8 1.80E−09 −0.458268807 0.651 0.725 Atp5j2 1.95E−09 −0.459501596 0.54 0.655 Uqcrh 9.19E−10 −0.460044483 0.54 0.64 Atp6v1f 6.68E−07 −0.460322844 0.169 0.255 Tyms 0.003364971 −0.461312009 0.079 0.16 Birc5 0.002080218 −0.461323711 0.037 0.135 1810009A15Rik 0.000873289 −0.462298376 0.085 0.145 Nhp2l1 0.000111665 −0.462353491 0.021 0.135 Acss2 0.001170604 −0.462378608 0.042 0.135 Cth 0.000374245 −0.463058297 0.069 0.155 mt-Co3 1.81E−05 −0.464537778 0.365 0.465 Gm2000 0.000231137 −0.465125929 0.228 0.34 Cotl1 4.82E−05 −0.465958007 0.116 0.195 Acp1 0.000155081 −0.467085333 0.058 0.135 Gm15013 7.05E−06 −0.468197025 0.011 0.105 Slc35b2 2.61E−06 −0.46848618 0.074 0.125 Rps3a3 0.000817177 −0.468723482 0.069 0.2 Sltm 0.000349106 −0.46911727 0.111 0.18 Hn1 1.86E−05 −0.469390434 0.196 0.27 Eef1g 1.00E−08 −0.469750373 0.444 0.53 Asns 9.62E−05 −0.471303481 0.19 0.275 Tpsg1 0.000363266 −0.471901739 0.048 0.13 Dak 0.007874916 −0.472124737 0.09 0.18 Gm16477 1.08E−06 −0.472565431 0 0.11 Ndufv2 7.09E−07 −0.473290774 0.243 0.365 1110004F10Rik 9.58E−05 −0.474609204 0.095 0.155 Gng5 3.09E−06 −0.479960246 0.164 0.245 Ndufaf2 0.004110958 −0.479975335 0.069 0.135 Ndufa13 1.66E−07 −0.48083147 0.402 0.49 Gm23061 7.14E−05 −0.482775907 0.016 0.125 Shmt2 8.01E−05 −0.483080489 0.074 0.16 Gm10076 1.72E−10 −0.484503743 0.45 0.56 Cdca3 6.36E−05 −0.484624632 0.042 0.125 Cbx5 4.00E−05 −0.485128427 0.111 0.215 Eif3f 1.43E−06 −0.485424802 0.296 0.385 Pck2 0.000208141 −0.485540607 0.053 0.145 Eprs 6.89E−08 −0.485931753 0.228 0.29 Gm10020 0.000108183 −0.487004123 0.016 0.105 Tecr 3.14E−05 −0.487182978 0.138 0.2 Rangap1 0.000162202 −0.487612162 0.095 0.155 Tmem205 0.000121965 −0.487850162 0.101 0.185 Nop58 0.000225767 −0.489454013 0.206 0.29 Pcna-ps2 8.85E−06 −0.489873887 0.005 0.11 Pklr 0.002367444 −0.491970544 0.058 0.15 Lsm4 9.53E−05 −0.492705301 0.233 0.315 Atp5l 0.000539431 −0.49273644 0.101 0.205 Gstm1 0.000272395 −0.493816218 0.026 0.145 Psmd7 1.48E−06 −0.493969285 0.164 0.22 Fh1 0.000202604 −0.49442165 0.095 0.17 Tmsb4x 4.43E−11 −0.49479822 0.651 0.79 Fgfbp1 0.000750633 −0.495437365 0.085 0.18 Atf4 2.88E−07 −0.496445223 0.36 0.46 Areg 0.000275857 −0.49685122 0.053 0.17 Fcf1 0.000162147 −0.497021273 0.058 0.12 Mrpl51 7.33E−06 −0.497538972 0.095 0.165 Smchd1 0.002305186 −0.498378269 0.053 0.12 Polr2j 0.000684831 −0.498673938 0.111 0.185 Pfkl 6.73E−05 −0.499634165 0.042 0.135 Prdx6 4.07E−06 −0.500505721 0.249 0.33 Cyb5 3.57E−05 −0.500808599 0.228 0.305 Ankrd11 0.002369846 −0.501490943 0.085 0.185 Eif4a1 2.86E−06 −0.501859788 0.28 0.37 Naa38 3.74E−05 −0.502212809 0.069 0.195 Magoh 0.000587613 −0.502865808 0.159 0.26 Wdr18 0.001085917 −0.503215799 0.032 0.12 Srsf7 2.81E−05 −0.50490254 0.18 0.28 Smc4 8.64E−06 −0.505173492 0.132 0.185 Gstt2 0.000561655 −0.506462769 0.063 0.175 Cdk1 0.000146053 −0.508137557 0.021 0.14 Rps21 5.63E−12 −0.509661685 0.725 0.84 Psma2 7.00E−07 −0.509671402 0.354 0.425 Cetn3 0.000326123 −0.50981447 0.164 0.245 Rps18 4.49E−15 −0.51110149 0.788 0.91 Gm11808 5.65E−05 −0.511808741 0.069 0.18 Cldn4 1.30E−07 −0.51370029 0.153 0.22 Pdk1 3.35E−05 −0.513914438 0.032 0.15 Rpl21 7.70E−06 −0.513972335 0.058 0.175 Snrpe 1.74E−05 −0.516593931 0.238 0.34 Gm8444 1.08E−06 −0.51667756 0.085 0.19 Mrps21 1.48E−06 −0.521055466 0.127 0.19 Sc4mol 0.000468775 −0.521179845 0.111 0.21 Mki67 0.000338076 −0.522404477 0.116 0.22 Psma6 8.62E−09 −0.522605652 0.228 0.305 Gm11273 0.00020713 −0.523567879 0.026 0.14 Clca4 1.14E−05 −0.523666086 0.291 0.405 Nars 6.49E−09 −0.524789582 0.397 0.49 Tcp1 5.32E−05 −0.525377019 0.19 0.3 Polr2f 1.53E−07 −0.525945365 0.228 0.315 Eif3k 4.38E−07 −0.526346694 0.254 0.325 Nap1l1 2.19E−05 −0.527538598 0.09 0.185 Tomm70a 9.27E−06 −0.527579374 0.132 0.22 Yeats4 2.31E−06 −0.527655223 0.058 0.12 Stoml2 4.16E−05 −0.527839292 0.042 0.165 2810417H13Rik 0.001607571 −0.52804929 0.101 0.185 Hells 0.000243783 −0.529360928 0.058 0.165 Ndufa6 1.40E−12 −0.533999242 0.545 0.65 AC102758.1 2.63E−07 −0.534923967 0 0.12 2700094K13Rik 0.000512807 −0.535013337 0.09 0.205 Pdgfa 1.19E−05 −0.536558959 0.063 0.175 Ndrg1 6.05E−08 −0.537273895 0.159 0.25 Sf3b5 9.20E−05 −0.537490233 0.148 0.265 Nucks1 1.24E−06 −0.538891601 0.148 0.22 Swi5 4.77E−08 −0.541198142 0.212 0.28 Uqcrb 7.34E−08 −0.541280369 0.265 0.33 Gm10288 8.91E−05 −0.542500756 0.058 0.17 Hnrnpab 1.31E−07 −0.54318878 0.302 0.375 Slc20a1 4.53E−06 −0.543898499 0.021 0.165 Cox7b 2.27E−08 −0.545343393 0.561 0.675 Ndufa7 2.99E−09 −0.545820272 0.418 0.49 Tuba1c 1.04E−08 −0.549013752 0.265 0.325 Rsl1d1 6.88E−06 −0.549358007 0.233 0.33 mt-Nd6 1.16E−05 −0.549641911 0.095 0.235 Fcgbp 5.95E−09 −0.549750762 0.291 0.52 Tm4sf20 2.84E−05 −0.549763824 0.228 0.305 Rbx1 3.12E−06 −0.551654044 0.169 0.28 Ccnd2 4.94E−05 −0.551933365 0.19 0.325 Nhp2 1.70E−06 −0.55337121 0.196 0.29 Eif3m 5.72E−08 −0.55339479 0.159 0.26 Cyp51 1.22E−05 −0.554103319 0.138 0.23 Ddit4 2.46E−06 −0.555502258 0.143 0.25 Top2a 0.001567232 −0.555561891 0.143 0.255 BC003965 0.000266797 −0.559685008 0.053 0.155 Smarcc1 2.83E−07 −0.560608277 0.079 0.18 Rpl9 0.000271667 −0.561257384 0.074 0.19 Hspa9 1.67E−07 −0.56195966 0.307 0.37 Ccdc34 9.27E−07 −0.564514804 0.148 0.24 Gm12728 5.87E−07 −0.565583001 0.021 0.155 Mrp63 4.92E−07 −0.565784445 0.18 0.255 Hook1 9.72E−09 −0.565962572 0.354 0.43 Ran 1.51E−05 −0.567446092 0.201 0.295 Eif4ebp1 2.02E−06 −0.567805133 0.132 0.245 Ankrd37 1.81E−06 −0.568385883 0.016 0.115 Rplp2 3.67E−13 −0.568701153 0.772 0.83 Prdx4 4.04E−05 −0.568737278 0.069 0.195 Ppdpf 3.75E−06 −0.569191101 0.074 0.205 Vaultrc5 2.37E−07 −0.569267163 0.185 0.335 Fasn 4.42E−05 −0.569471635 0.026 0.155 Mrpl36 5.05E−05 −0.57001908 0.101 0.19 Krtcap2 6.02E−08 −0.571380129 0.254 0.365 Cct5 8.16E−08 −0.572992216 0.312 0.445 Pgls 1.99E−08 −0.573511636 0.228 0.31 Rpa3 1.19E−05 −0.574575445 0.127 0.235 Eif3c 1.32E−09 −0.574719054 0.312 0.38 Mrpl17 4.29E−06 −0.575838065 0.148 0.23 Mki67ip 1.12E−05 −0.576197418 0.058 0.165 Pgk1 3.33E−08 −0.585357423 0.011 0.175 S100a11 8.20E−06 −0.586880309 0.053 0.205 Ssr2 1.56E−09 −0.587438682 0.354 0.415 Gm8420 3.83E−08 −0.587473026 0.048 0.18 Gm16519 4.26E−07 −0.587507744 0.005 0.14 Prdx1 1.85E−13 −0.587905501 0.709 0.82 Tmem14c 1.00E−05 −0.588165576 0.111 0.21 Ftl1 1.88E−07 −0.589908505 0.201 0.33 Rpl15 7.25E−07 −0.59009606 0.079 0.21 Nme1 6.20E−08 −0.591521443 0.323 0.455 Rpl23a-ps3 3.00E−07 −0.592301497 0.005 0.15 Gstp1 3.83E−06 −0.592934613 0.132 0.28 Eml4 2.92E−06 −0.593265524 0.18 0.3 Gm17541 1.70E−05 −0.594037036 0.042 0.195 Ndufb11 4.13E−07 −0.594473406 0.307 0.435 Rps23 6.24E−06 −0.595046667 0.069 0.195 Avpi1 1.76E−08 −0.596459688 0.048 0.175 Pcsk9 3.38E−07 −0.59674704 0.005 0.135 Psmb6 1.17E−06 −0.596971787 0.254 0.35 Psma4 8.41E−10 −0.597387553 0.259 0.405 Ifitm2 1.03E−09 −0.598786595 0.228 0.35 Cfl1 3.22E−07 −0.600313526 0.233 0.365 Mrpl13 0.000371267 −0.601725408 0.095 0.2 Sox4 5.16E−06 −0.603429861 0.069 0.165 Mcm6 1.72E−06 −0.603547383 0.042 0.145 Srsf3 1.95E−07 −0.6039602 0.312 0.42 H3f3a 6.49E−09 −0.604007875 0.18 0.345 Rbm39 1.17E−09 −0.606043989 0.37 0.425 Eif2s2 5.24E−10 −0.607068949 0.265 0.325 Rpl22l1 2.45E−09 −0.609051327 0.471 0.6 Rpl37 1.17E−08 −0.610075998 0.365 0.57 Rpl35 1.95E−10 −0.610353294 0.508 0.67 Rpl36al 7.33E−11 −0.610486021 0.434 0.565 Dut 7.95E−05 −0.612192819 0.085 0.205 Cdk4 2.45E−07 −0.614018654 0.196 0.31 Atp5h 2.86E−08 −0.614183227 0.381 0.55 Psat1 1.39E−05 −0.615721908 0.021 0.135 Rpl23a 6.00E−06 −0.617198542 0.069 0.205 Cct6a 5.86E−09 −0.617549769 0.19 0.32 Rps15a 3.21E−17 −0.617950261 0.725 0.885 Utp11l 2.21E−06 −0.620348167 0.053 0.155 H2afz 1.59E−05 −0.622245697 0.074 0.22 Malat1 8.65E−18 −0.622877884 0.825 0.95 Tceb1 7.01E−08 −0.62356922 0.127 0.22 Rps19 2.21E−22 −0.626883398 0.778 0.935 Cystm1 8.21E−07 −0.629720696 0.27 0.48 Snrpd1 5.61E−06 −0.630109732 0.175 0.31 Taf1d 2.26E−06 −0.635069863 0.116 0.28 Rpl22 4.49E−11 −0.635175288 0.571 0.71 Gm8226 1.68E−09 −0.636342072 0 0.155 Atpif1 3.12E−16 −0.636535803 0.614 0.715 Rps26 1.20E−13 −0.636580958 0.64 0.85 Romo1 6.98E−07 −0.636823826 0.164 0.29 Mrps14 1.65E−07 −0.640726979 0.217 0.33 H2afj 1.71E−10 −0.646903336 0.386 0.525 Calml4 3.18E−07 −0.647748686 0.328 0.435 1110038B12Rik 2.16E−05 −0.648324894 0.19 0.33 Gm10269 9.46E−08 −0.648683508 0.185 0.335 Gm7808 1.55E−07 −0.655072973 0.153 0.3 Grcc10 1.10E−06 −0.656610053 0.042 0.195 0610009D07Rik 1.48E−07 −0.657728458 0.122 0.26 Dynll1 6.27E−11 −0.662579856 0.27 0.37 Ddx21 1.31E−05 −0.662956383 0.127 0.22 Rpph1 1.55E−06 −0.66500112 0.206 0.35 Gm9396 1.83E−10 −0.667349981 0 0.17 Gm10260 4.78E−08 −0.66852283 0.19 0.32 Snhg3 2.14E−05 −0.668806581 0.053 0.165 Gm10704 1.24E−08 −0.669633097 0.048 0.205 Actg1 3.64E−08 −0.670416972 0.063 0.195 Tmbim4 5.61E−11 −0.671558907 0.164 0.3 Rpl8 2.27E−19 −0.673589579 0.841 0.93 Pglyrp1 1.08E−12 −0.674095426 0.286 0.38 Tmpo 4.88E−08 −0.674296706 0.106 0.26 Ndufb5 1.69E−07 −0.675956675 0.238 0.375 Hmgcs1 3.71E−08 −0.681395435 0.18 0.31 Fkbp3 9.67E−08 −0.683013521 0.217 0.365 Tubb4b 6.55E−07 −0.6830716 0.238 0.36 Tceb2 4.28E−08 −0.683897902 0.254 0.36 Rps14 3.75E−35 −0.685397949 0.942 1 Pebp1 1.09E−06 −0.686785465 0.085 0.26 Ranbp1 2.17E−07 −0.689278828 0.238 0.4 Aldob 2.10E−07 −0.689756337 0.423 0.51 Fundc2 7.28E−06 −0.692795472 0.09 0.235 Rps13 2.33E−07 −0.6933494 0.053 0.235 Nop10 8.07E−09 −0.698210368 0.302 0.435 Ubb 9.78E−14 −0.699686199 0.534 0.72 Rpl11 2.25E−08 −0.700723709 0.079 0.245 Rpl36a 1.95E−08 −0.701466664 0.063 0.235 Ssb 3.17E−09 −0.70170735 0.275 0.365 Rplp0 1.31E−24 −0.702831276 0.889 0.98 Fdft1 2.85E−09 −0.705422138 0.026 0.18 Sod1 4.95E−09 −0.706167279 0.339 0.5 Chchd2 3.49E−14 −0.7100971 0.556 0.66 Gm8186 1.37E−11 −0.714755531 0.058 0.265 Oaz1 1.71E−11 −0.716097575 0.339 0.515 Rpl9-ps6 9.23E−11 −0.718652704 0.228 0.41 Adh1 7.58E−07 −0.718939375 0.021 0.175 Dbi 1.76E−12 −0.721709502 0.54 0.7 Bsg 3.13E−17 −0.725739341 0.561 0.7 Pcna 3.16E−08 −0.727067188 0.032 0.22 Cd81 4.29E−07 −0.727642531 0.143 0.305 Rps3 1.18E−35 −0.728040462 0.868 0.955 Ndufc2 3.90E−11 −0.732825784 0.286 0.435 Rpl4 2.16E−29 −0.732837039 0.862 0.96 Mrpl18 3.39E−06 −0.735394926 0.101 0.23 Lrrc58 8.20E−10 −0.735447558 0.222 0.44 Orc5 1.54E−07 −0.736124896 0.116 0.31 Eef1d 8.14E−12 −0.73613252 0.222 0.375 Gm17087 1.56E−10 −0.736677957 0.074 0.26 Tomm5 8.27E−09 −0.737516923 0.153 0.28 Rps27l 6.13E−19 −0.737787094 0.63 0.755 Rpl19 6.63E−10 −0.740440475 0.143 0.38 Rpl9-ps1 5.47E−10 −0.740929464 0.058 0.23 Tubb5 3.16E−07 −0.741863963 0.275 0.47 Tomm20 4.91E−08 −0.743078547 0.063 0.23 Gm10132 1.51E−09 −0.744416506 0.016 0.195 Hsp90aa1 2.17E−08 −0.750639113 0.217 0.395 Gpx2 8.61E−15 −0.753317799 0.534 0.73 Ifitm3 1.90E−07 −0.754046651 0.048 0.215 Nme2 3.36E−09 −0.762130663 0.037 0.24 Txn1 1.13E−16 −0.763435316 0.582 0.74 Gm21957 6.44E−12 −0.763632491 0.021 0.24 Hspe1 2.73E−10 −0.763729014 0.307 0.505 Gm10036 8.61E−10 −0.775609028 0.079 0.3 BX465866.1 5.39E−11 −0.778403388 0.005 0.21 Rpl5 5.26E−10 −0.782091406 0.032 0.25 Reg1 3.08E−08 −0.787506491 0 0.135 Banf1 1.48E−11 −0.789476706 0.243 0.4 Ccl9 3.27E−07 −0.792780324 0.159 0.29 Chga 3.96E−06 −0.793861188 0.021 0.14 Atp5g1 1.38E−09 −0.793991628 0.116 0.305 Rpl21-ps4 8.54E−11 −0.796368647 0.042 0.23 Mrpl42 6.44E−07 −0.796407767 0.095 0.285 Gm8225 1.36E−08 −0.796678298 0.032 0.21 Gm10250 2.26E−09 −0.799321997 0.111 0.325 Bnip3 3.54E−11 −0.802498019 0.011 0.205 mt-Atp6 3.27E−09 −0.803188824 0.101 0.36 Gm24245 2.52E−08 −0.804754086 0.095 0.29 Ero1l 8.42E−11 −0.808827653 0.058 0.205 2700060E02Rik 6.36E−12 −0.809707393 0.185 0.375 Hmgn1 1.17E−08 −0.818283446 0.164 0.37 Ptma 2.14E−16 −0.819418803 0.413 0.6 Rpl23 3.11E−14 −0.820359999 0.429 0.7 1810022K09Rik 2.80E−09 −0.824323285 0.138 0.325 Amica1 4.48E−08 −0.825072785 0.053 0.245 Gm24146 1.51E−10 −0.82659799 0.005 0.2 Prelid1 2.69E−12 −0.828185548 0.18 0.355 Ube2c 4.07E−08 −0.841087055 0.063 0.26 Rpl29 5.87E−12 −0.845848483 0.243 0.495 Myl6 2.92E−13 −0.846731289 0.106 0.32 Snrpg 5.91E−10 −0.853050582 0.143 0.365 Rps2-ps10 2.46E−13 −0.855611608 0.005 0.245 Rpl12 9.24E−11 −0.860202503 0.079 0.31 Rpl10a 1.83E−09 −0.865535687 0.106 0.33 Gapdh 9.03E−12 −0.867175893 0.005 0.21 Rpl13a 1.87E−30 −0.867533003 0.825 0.98 Uqcc2 5.42E−10 −0.871542218 0.18 0.355 Fxyd3 1.05E−13 −0.874025559 0.265 0.4 Rps25 4.73E−12 −0.875372311 0.228 0.51 Wdr89 5.09E−13 −0.8772842 0.233 0.5 Gpi1 1.02E−13 −0.88042701 0.148 0.385 Ncl 4.93E−19 −0.888155805 0.577 0.765 Rpl14 4.89E−26 −0.88889146 0.667 0.93 Rps27a 1.86E−13 −0.891977047 0.143 0.385 Gas5 2.89E−16 −0.893410101 0.455 0.705 mt-Nd4 5.56E−22 −0.895096253 0.714 0.905 Btf3 2.34E−12 −0.895141698 0.185 0.38 mt-Nd2 1.69E−21 −0.898574406 0.683 0.9 Rpl13-ps3 5.10E−11 −0.900883199 0.111 0.34 Rpl26 2.06E−28 −0.905611362 0.735 0.96 Npm1 1.52E−16 −0.906073879 0.418 0.68 Gm5786 4.79E−11 −0.907534399 0.032 0.26 Rpsa-ps10 2.74E−13 −0.907911938 0.011 0.25 Gm5619 1.70E−15 −0.909743635 0 0.245 Rpl30 2.32E−14 −0.910450661 0.254 0.46 Rpl38 5.24E−21 −0.911300739 0.54 0.785 Rps10-ps1 6.46E−15 −0.912387807 0.233 0.51 Tpi1 3.85E−18 −0.912837229 0.354 0.63 Rpl32 4.10E−48 −0.915624328 0.91 0.99 Gm20594 1.19E−12 −0.915936193 0.016 0.24 Tuba1b 1.77E−09 −0.919547117 0.101 0.345 Rnase1 3.84E−09 −0.920553754 0.164 0.325 Fdps 5.76E−11 −0.92143491 0.048 0.3 Rps17 3.99E−12 −0.927361901 0.058 0.315 Rps24 3.23E−44 −0.92858835 0.852 0.985 Gm9765 2.15E−15 −0.935465649 0.206 0.405 Rn7sk 1.83E−10 −0.935482095 0.413 0.67 Fabp1 2.90E−08 −0.962647304 0.138 0.295 Rps2 2.28E−32 −0.969513628 0.725 0.95 Gm26917 8.57E−11 −0.975909586 0.048 0.265 Naca 5.88E−18 −0.976691391 0.365 0.655 Rpl27a 4.20E−16 −0.98731053 0.196 0.5 Rps9 1.03E−35 −0.991425345 0.778 0.98 Rgcc 1.82E−12 −0.998185133 0.101 0.35 Rpl13a-ps1 9.79E−14 −1.004455068 0.085 0.385 Ckb 1.08E−14 −1.009532596 0.048 0.29 Fam162a 1.13E−12 −1.012037257 0.111 0.37 Rpl10 1.07E−13 −1.022990312 0.063 0.335 Hmgb2 6.56E−13 −1.025038207 0.159 0.41 Tac1 1.29E−07 −1.030418687 0 0.125 Gm4968 4.37E−18 −1.032143247 0.021 0.345 Rps3a1 5.74E−30 −1.044284182 0.603 0.865 Eef1b2 4.34E−32 −1.04512757 0.635 0.9 Gm6472 3.88E−14 −1.048488978 0.037 0.3 Rpl6 5.47E−18 −1.0518541 0.196 0.515 Rpl18 4.56E−23 −1.060753594 0.291 0.625 Gnb2l1 1.02E−38 −1.072659987 0.725 0.93 Klk1 5.35E−11 −1.075285863 0.122 0.385 Rps15 7.56E−32 −1.079539296 0.571 0.85 Tmsb10 6.52E−25 −1.08589897 0.333 0.61 Rplp1 2.63E−51 −1.092634805 0.878 0.985 mt-Nd5 5.47E−27 −1.09416199 0.598 0.875 Rps11 1.31E−31 −1.124264453 0.593 0.895 Rps10 2.72E−38 −1.147671836 0.614 0.9 Rps4x 7.61E−23 −1.147709224 0.228 0.6 Rps16 6.32E−19 −1.147777751 0.175 0.525 Rps5 5.05E−52 −1.165218291 0.862 0.995 Gm6576 2.63E−20 −1.168707414 0.085 0.455 Rpl18a 1.01E−27 −1.179638123 0.376 0.79 Gm5160 1.89E−16 −1.182020528 0.048 0.385 Scd2 1.79E−19 −1.186244206 0.079 0.445 mt-Co1 2.35E−40 −1.190862701 0.72 0.95 Eno1 2.35E−21 −1.209794757 0.032 0.36 Rpl10-ps3 1.38E−21 −1.2108781 0.032 0.41 Rpl3 1.77E−26 −1.215044536 0.333 0.755 Pkm 4.44E−20 −1.222324635 0.19 0.56 Ldha 6.40E−39 −1.237276982 0.508 0.84 mt-Cytb 3.39E−53 −1.237635959 0.878 0.99 Gm9843 2.41E−33 −1.248833345 0.481 0.815 Rpsa 2.79E−25 −1.260253035 0.228 0.655 Rps8 4.91E−35 −1.26046721 0.503 0.835 Eef1a1 4.73E−63 −1.262523757 0.772 0.995 Gm10275 4.82E−24 −1.263892591 0.095 0.475 Gm23935 1.82E−41 −1.30516138 0.762 0.94 Rpl13 5.82E−43 −1.306098605 0.561 0.915 Mif 9.40E−23 −1.370920115 0.106 0.485 Rps6 2.16E−24 −1.378898393 0.063 0.52 Ppia 1.87E−20 −1.387574713 0.058 0.44 Gip 2.45E−06 −1.444689624 0.021 0.12 Gm9493 7.55E−26 −1.461422006 0.048 0.485 Rps7 8.10E−43 −1.467472606 0.365 0.795 Rps20 5.68E−65 −1.472318469 0.656 0.975 mt-Nd1 1.10E−62 −1.493267245 0.852 0.995 Rpl7a 3.66E−31 −1.493650494 0.116 0.635 Uba52 1.20E−36 −1.495718174 0.259 0.76 Mt1 8.51E−39 −1.566984123 0.365 0.82 Aldoa 6.68E−41 −1.581290123 0.265 0.745 Gm8730 1.14E−42 −1.651230838 0.206 0.8 Rpl7 9.55E−52 −1.695523228 0.349 0.865 Tpt1 4.70E−51 −1.766089197 0.286 0.79 Xist 1.61E−43 −1.856025581 0 0.58 Mt2 1.87E−44 −2.004274188 0.079 0.7 Chgb 1.68E−16 −2.00780355 0.011 0.28 Table 1D. ROC-test on ENR+CV, ENR, and ENR+CD organoids to determine cluster-enriched marker genes (FIG. 4D ENR+CV, ENR, ENR+CD) myAUC avg_diff power pct.1 pct.2 cluster gene Rpph1 0.986 3.319373077 0.972 1 0.382 ENR+CV-1 Rpph1 Gm26924 0.956 1.658756335 0.912 1 0.936 ENR+CV-1 Gm26924 Rn7sk 0.949 3.047657851 0.898 0.989 0.546 ENR+CV-1 Rn7sk Snord13 0.919 2.638557932 0.838 0.899 0.168 ENR+CV-1 Snord13 Gm15564 0.914 2.398421613 0.828 0.911 0.205 ENR+CV-1 Gm15564 Lars2 0.91 1.723005835 0.82 0.989 0.604 ENR+CV-1 Lars2 Gm24616 0.899 2.923018252 0.798 0.81 0.028 ENR+CV-1 Gm24616 Vaultrc5 0.879 2.060246989 0.758 0.872 0.285 ENR+CV-1 Vaultrc5 Snord118 0.867 2.548026049 0.734 0.788 0.107 ENR+CV-1 Snord118 Rny1 0.864 2.437116646 0.728 0.765 0.08 ENR+CV-1 Rny1 Gm24146 0.856 2.241813583 0.712 0.788 0.154 ENR+CV-1 Gm24146 n-R5-8s1 0.853 2.496592253 0.706 0.726 0.032 ENR+CV-1 n-R5-8s1 Gm26917 0.852 1.955131302 0.704 0.855 0.317 ENR+CV-1 Gm26917 Gm24601 0.82 2.13893558 0.64 0.659 0.028 ENR+CV-1 Gm24601 Gm23037 0.817 2.378194081 0.634 0.665 0.055 ENR+CV-1 Gm23037 Pabpc1 0.812 0.838615671 0.624 0.966 0.8 ENR+CV-1 Pabpc1 Gm26205 0.805 2.694605811 0.61 0.631 0.039 ENR+CV-1 Gm26205 Gm23924 0.758 2.278844246 0.516 0.52 0.006 ENR+CV-1 Gm23924 mmu-mir-6236 0.746 1.51273369 0.492 0.531 0.052 ENR+CV-1 mmu-mir-6236 Gm23973 0.741 1.661730228 0.482 0.497 0.02 ENR+CV-1 Gm23973 Tpi1 0.741 0.890232989 0.482 0.866 0.588 ENR+CV-1 Tpi1 Gm23935 0.74 0.938297465 0.48 1 0.932 ENR+CV-1 Gm23935 Rny3 0.739 1.501659109 0.478 0.553 0.1 ENR+CV-1 Rny3 Rpl41 0.725 0.720514673 0.45 0.944 0.825 ENR+CV-1 Rpl41 Bsg 0.722 0.900022309 0.444 0.849 0.733 ENR+CV-1 Bsg Gpi1 0.719 0.943848591 0.438 0.721 0.385 ENR+CV-1 Gpi1 Neat1 0.718 1.153263742 0.436 0.575 0.16 ENR+CV-1 Neat1 Rrbp1 0.711 0.791087255 0.422 0.749 0.436 ENR+CV-1 Rrbp1 Gm23731 0.707 1.685390231 0.414 0.419 0.007 ENR+CV-1 Gm23731 Ero1l 0.707 1.269058774 0.414 0.559 0.182 ENR+CV-1 Ero1l mt-Tc 0.701 1.173516039 0.402 0.458 0.062 ENR+CV-1 mt-Tc Egr1 0.695 0.88360283 0.39 0.676 0.401 ENR+CV-1 Egr1 Gm2000 0.692 0.775271431 0.384 0.726 0.447 ENR+CV-1 Gm2000 Pabpc4 0.69 1.055382571 0.38 0.525 0.179 ENR+CV-1 Pabpc4 Gm24289 0.686 1.507727803 0.372 0.385 0.018 ENR+CV-1 Gm24289 Gm22620 0.684 1.544347591 0.368 0.374 0.008 ENR+CV-1 Gm22620 Rpl37a 0.682 0.634110211 0.364 0.788 0.593 ENR+CV-1 Rpl37a Gm26339 0.681 1.286835564 0.362 0.391 0.032 ENR+CV-1 Gm26339 Gm22982 0.68 1.358383995 0.36 0.385 0.029 ENR+CV-1 Gm22982 Atp5d 0.678 0.612211468 0.356 0.704 0.425 ENR+CV-1 Atp5d H2-Q10 0.677 0.998914091 0.354 0.464 0.125 ENR+CV-1 H2-Q10 Ndufv3 0.677 0.734944941 0.354 0.626 0.327 ENR+CV-1 Ndufv3 H1f0 0.677 0.719102822 0.354 0.67 0.381 ENR+CV-1 H1f0 Gm25538 0.676 1.398247413 0.352 0.363 0.014 ENR+CV-1 Gm25538 Hes1 0.671 0.868351272 0.342 0.542 0.227 ENR+CV-1 Hes1 Ubc 0.671 0.631162449 0.342 0.754 0.567 ENR+CV-1 Ubc Scd2 0.671 0.63057596 0.342 0.76 0.531 ENR+CV-1 Scd2 Pkm 0.67 0.596380704 0.34 0.782 0.641 ENR+CV-1 Pkm Scd1 0.668 1.090989415 0.336 0.425 0.102 ENR+CV-1 Scd1 n-R5s2 0.665 1.323674266 0.33 0.341 0.013 ENR+CV-1 n-R5s2 Gm25541 0.661 1.231078118 0.322 0.33 0.01 ENR+CV-1 Gm25541 Aes 0.66 0.818117808 0.32 0.531 0.255 ENR+CV-1 Aes Junb 0.66 0.71068372 0.32 0.648 0.385 ENR+CV-1 Junb Gm22063 0.658 1.272082171 0.316 0.33 0.015 ENR+CV-1 Gm22063 Gm26035 0.657 1.321304052 0.314 0.318 0.006 ENR+CV-1 Gm26035 Gm22307 0.657 1.238608875 0.314 0.324 0.011 ENR+CV-1 Gm22307 Jun 0.656 0.613726056 0.312 0.743 0.542 ENR+CV-1 Jun Galk1 0.655 0.78447389 0.31 0.48 0.196 ENR+CV-1 Galk1 n-R5s193 0.654 1.138720844 0.308 0.318 0.011 ENR+CV-1 n-R5s193 Gm24336 0.653 1.206891752 0.306 0.318 0.016 ENR+CV-1 Gm24336 Gm22633 0.651 1.239750758 0.302 0.307 0.005 ENR+CV-1 Gm22633 mt-Tp 0.649 1.140133173 0.298 0.341 0.047 ENR+CV-1 mt-Tp Atf4 0.649 0.609094522 0.298 0.654 0.442 ENR+CV-1 Atf4 H2afj 0.648 0.561595967 0.296 0.721 0.503 ENR+CV-1 H2afj Gm25588 0.647 1.145184011 0.294 0.296 0.002 ENR+CV-1 Gm25588 Pdap1 0.647 0.59265881 0.294 0.648 0.409 ENR+CV-1 Pdap1 Gm25822 0.646 1.020422353 0.292 0.335 0.047 ENR+CV-1 Gm25822 Eef2 0.646 0.369209213 0.292 0.916 0.849 ENR+CV-1 Eef2 Snord35a 0.645 1.136681512 0.29 0.302 0.014 ENR+CV-1 Snord35a Snora68 0.643 1.091810479 0.286 0.313 0.031 ENR+CV-1 Snora68 Bola2 0.643 0.675089957 0.286 0.553 0.304 ENR+CV-1 Bola2 mt-Tq 0.641 1.089303891 0.282 0.318 0.042 ENR+CV-1 mt-Tq Snord49b 0.641 1.000738074 0.282 0.324 0.047 ENR+CV-1 Snord49b Ppp2r3a 0.641 0.826612201 0.282 0.374 0.102 ENR+CV-1 Ppp2r3a Por 0.64 0.781992824 0.28 0.43 0.167 ENR+CV-1 Por Tkt 0.639 0.561209409 0.278 0.642 0.466 ENR+CV-1 Tkt Rnu3a 0.637 1.076134966 0.274 0.296 0.024 ENR+CV-1 Rnu3a mt-Tm 0.635 1.007755682 0.27 0.296 0.031 ENR+CV-1 mt-Tm Gm26335 0.634 1.175296399 0.268 0.274 0.006 ENR+CV-1 Gm26335 Gm24044 0.634 1.138065841 0.268 0.274 0.006 ENR+CV-1 Gm24044 Slc25a1 0.634 0.705016848 0.268 0.453 0.202 ENR+CV-1 Slc25a1 Elf3 0.634 0.647172014 0.268 0.531 0.299 ENR+CV-1 Elf3 Mir5136 0.632 0.774248421 0.264 0.38 0.125 ENR+CV-1 Mir5136 Pcsk9 0.632 0.761198774 0.264 0.419 0.169 ENR+CV-1 Pcsk9 Slc16a3 0.631 0.79340192 0.262 0.363 0.108 ENR+CV-1 Slc16a3 Gm23248 0.63 1.151415243 0.26 0.263 0.002 ENR+CV-1 Gm23248 Gm22748 0.63 1.074148554 0.26 0.268 0.008 ENR+CV-1 Gm22748 Insig1 0.63 0.767669394 0.26 0.408 0.166 ENR+CV-1 Insig1 Ier2 0.63 0.505662744 0.26 0.698 0.536 ENR+CV-1 Ier2 Rmrp 0.629 1.126647888 0.258 0.268 0.011 ENR+CV-1 Rmrp Fasn 0.629 0.739065288 0.258 0.385 0.141 ENR+CV-1 Fasn Gcat 0.628 0.692805606 0.256 0.413 0.176 ENR+CV-1 Gcat Kcnq1 0.627 0.6410026 0.254 0.402 0.159 ENR+CV-1 Kcnq1 Ptms 0.627 0.609672251 0.254 0.458 0.217 ENR+CV-1 Ptms Arpp19 0.627 0.493294604 0.254 0.581 0.351 ENR+CV-1 Arpp19 Hmgcs2 0.626 0.759089952 0.252 0.358 0.111 ENR+CV-1 Hmgcs2 Dhcr24 0.626 0.631557553 0.252 0.453 0.222 ENR+CV-1 Dhcr24 Atf3 0.625 0.643973891 0.25 0.486 0.258 ENR+CV-1 Atf3 Acot1 0.622 0.710419081 0.244 0.335 0.099 ENR+CV-1 Acot1 Mpnd 0.621 0.708997116 0.242 0.335 0.099 ENR+CV-1 Mpnd 2410015M20Rik 0.621 0.536752663 0.242 0.475 0.254 ENR+CV-1 2410015M20Rik Cs 0.62 0.568703916 0.24 0.469 0.243 ENR+CV-1 Cs Atp1a1 0.62 0.473515788 0.24 0.603 0.411 ENR+CV-1 Atp1a1 Mt1 0.62 0.445838672 0.24 0.816 0.662 ENR+CV-1 Mt1 mt-Tv 0.619 0.81271412 0.238 0.279 0.043 ENR+CV-1 mt-Tv P4hb 0.619 0.586657125 0.238 0.715 0.594 ENR+CV-1 P4hb Egln3 0.618 0.799738642 0.236 0.302 0.069 ENR+CV-1 Egln3 Gm24018 0.617 0.993377346 0.234 0.24 0.006 ENR+CV-1 Gm24018 Rpn1 0.617 0.428805504 0.234 0.592 0.379 ENR+CV-1 Rpn1 Lonp1 0.616 0.589583395 0.232 0.408 0.186 ENR+CV-1 Lonp1 Btg2 0.615 0.633739142 0.23 0.441 0.234 ENR+CV-1 Btg2 Gm23624 0.614 1.000409547 0.228 0.235 0.006 ENR+CV-1 Gm23624 Tmem245 0.614 0.808401751 0.228 0.285 0.06 ENR+CV-1 Tmem245 Slc1a5 0.614 0.66247978 0.228 0.425 0.224 ENR+CV-1 Slc1a5 Hist1h1d 0.613 0.912426636 0.226 0.318 0.102 ENR+CV-1 Hist1h1d Ccnd2 0.613 0.472375902 0.226 0.57 0.392 ENR+CV-1 Ccnd2 Ddx21 0.613 0.463809532 0.226 0.536 0.328 ENR+CV-1 Ddx21 Mir3068 0.612 1.512462215 0.224 0.229 0.007 ENR+CV-1 Mir3068 Xist 0.612 0.358497733 0.224 0.838 0.675 ENR+CV-1 Xist Gm23792 0.611 1.204540163 0.222 0.223 0.002 ENR+CV-1 Gm23792 Aldh9a1 0.611 0.545665229 0.222 0.397 0.183 ENR+CV-1 Aldh9a1 Jund 0.611 0.500197084 0.222 0.441 0.226 ENR+CV-1 Jund Dbi 0.61 0.275424139 0.22 0.905 0.822 ENR+CV-1 Dbi Aqp1 0.609 0.695003335 0.218 0.363 0.157 ENR+CV-1 Aqp1 Hist1h1c 0.609 0.627009124 0.218 0.38 0.169 ENR+CV-1 Hist1h1c Snd1 0.609 0.551192281 0.218 0.408 0.204 ENR+CV-1 Snd1 Gm25080 0.608 1.067209442 0.216 0.218 0.002 ENR+CV-1 Gm25080 Gm22308 0.608 1.053725297 0.216 0.218 0.003 ENR+CV-1 Gm22308 Snhg9 0.607 0.585546114 0.214 0.413 0.221 ENR+CV-1 Snhg9 Gm24494 0.606 0.925369526 0.212 0.218 0.007 ENR+CV-1 Gm24494 Snord104 0.606 0.794148166 0.212 0.274 0.065 ENR+CV-1 Snord104 Pcyt2 0.606 0.561190093 0.212 0.38 0.176 ENR+CV-1 Pcyt2 Itpr3 0.606 0.549014385 0.212 0.324 0.113 ENR+CV-1 Itpr3 Mapk13 0.606 0.537793429 0.212 0.419 0.232 ENR+CV-1 Mapk13 Psmc1 0.606 0.496157383 0.212 0.447 0.248 ENR+CV-1 Psmc1 Pfkp 0.603 0.642014619 0.206 0.33 0.132 ENR+CV-1 Pfkp Gm24968 0.602 0.942841931 0.204 0.212 0.008 ENR+CV-1 Gm24968 Gm25835 0.601 0.981819841 0.202 0.207 0.004 ENR+CV-1 Gm25835 Snora47 0.601 0.956714744 0.202 0.207 0.004 ENR+CV-1 Snora47 Gm22003 0.601 0.925185229 0.202 0.207 0.005 ENR+CV-1 Gm22003 Slc39a14 0.601 0.790768526 0.202 0.268 0.072 ENR+CV-1 Slc39a14 Huwe1 0.601 0.51920054 0.202 0.419 0.232 ENR+CV-1 Huwe1 Sox4 0.601 0.447952131 0.202 0.553 0.376 ENR+CV-1 Sox4 Rpl411 0.923 1.449606719 0.846 0.985 0.819 ENR+CV-2 Rpl41 Pabpc11 0.886 1.104712088 0.772 0.982 0.794 ENR+CV-2 Pabpc1 Gm269241 0.885 1.229874544 0.77 1 0.934 ENR+CV-2 Gm26924 Gm20001 0.833 1.234565899 0.666 0.864 0.431 ENR+CV-2 Gm2000 Rpl37a1 0.811 1.085909223 0.622 0.867 0.583 ENR+CV-2 Rpl37a Rpl35a 0.797 0.820000153 0.594 0.938 0.781 ENR+CV-2 Rpl35a Rpph11 0.796 0.893345021 0.592 0.817 0.375 ENR+CV-2 Rpph1 Dbi1 0.77 0.665563321 0.54 0.959 0.816 ENR+CV-2 Dbi Uqcr10 0.763 0.754156685 0.526 0.914 0.666 ENR+CV-2 Uqcr10 Rpl37 0.76 0.827663322 0.52 0.853 0.651 ENR+CV-2 Rpl37 Gm155641 0.754 1.215487686 0.508 0.649 0.201 ENR+CV-2 Gm15564 Uqcr11 0.74 0.71183618 0.48 0.87 0.624 ENR+CV-2 Uqcr11 Rpl34 0.73 0.605848951 0.46 0.917 0.814 ENR+CV-2 Rpl34 Gm10076 0.727 0.7719867 0.454 0.808 0.609 ENR+CV-2 Gm10076 Taldo1 0.725 0.897515362 0.45 0.723 0.429 ENR+CV-2 Taldo1 Ifitm2 0.714 0.760262269 0.428 0.785 0.548 ENR+CV-2 Ifitm2 Cox4i1 0.714 0.511170832 0.428 0.953 0.851 ENR+CV-2 Cox4i1 Smoc2 0.708 0.82571651 0.416 0.729 0.438 ENR+CV-2 Smoc2 Cox6a1 0.703 0.555318243 0.406 0.888 0.7 ENR+CV-2 Cox6a1 Bex1 0.697 0.938299508 0.394 0.608 0.275 ENR+CV-2 Bex1 Uqcrq 0.696 0.535634296 0.392 0.897 0.756 ENR+CV-2 Uqcrq Tubb5 0.693 0.648505913 0.386 0.794 0.587 ENR+CV-2 Tubb5 Snord131 0.69 1.0744826 0.38 0.516 0.17 ENR+CV-2 Snord13 Tpi11 0.689 0.580926605 0.378 0.811 0.584 ENR+CV-2 Tpi1 H1f01 0.683 0.830904784 0.366 0.646 0.375 ENR+CV-2 H1f0 Atp5k 0.683 0.717227227 0.366 0.708 0.471 ENR+CV-2 Atp5k Rpl13 0.682 0.409862915 0.364 0.965 0.904 ENR+CV-2 Rpl13 Atp5e 0.676 0.519168361 0.352 0.82 0.667 ENR+CV-2 Atp5e Bola21 0.675 0.86455296 0.35 0.572 0.296 ENR+CV-2 Bola2 Aldoa 0.675 0.587357363 0.35 0.838 0.649 ENR+CV-2 Aldoa Eef21 0.67 0.409268422 0.34 0.917 0.847 ENR+CV-2 Eef2 2010107E04Rik 0.668 0.470785165 0.336 0.838 0.669 ENR+CV-2 2010107E04Rik Rpl18 0.665 0.497225913 0.33 0.817 0.665 ENR+CV-2 Rpl18 Fth1 0.664 0.513255274 0.328 0.879 0.824 ENR+CV-2 Fth1 Rpl35 0.664 0.49714052 0.328 0.805 0.715 ENR+CV-2 Rpl35 Vaultrc51 0.662 0.878420544 0.324 0.54 0.289 ENR+CV-2 Vaultrc5 Mif 0.66 0.577530321 0.32 0.717 0.502 ENR+CV-2 Mif Mlec 0.658 0.688143109 0.316 0.596 0.362 ENR+CV-2 Mlec Hmgcs21 0.656 1.05211155 0.312 0.395 0.102 ENR+CV-2 Hmgcs2 Pkm1 0.656 0.549587475 0.312 0.77 0.637 ENR+CV-2 Pkm Atp5b 0.647 0.391221588 0.294 0.844 0.727 ENR+CV-2 Atp5b Ndufb8 0.646 0.554698006 0.292 0.673 0.509 ENR+CV-2 Ndufb8 Ybx11 0.646 0.43841017 0.292 0.826 0.73 ENR+CV-2 Ybx1 Psma7 0.643 0.484191486 0.286 0.752 0.577 ENR+CV-2 Psma7 Wbp5 0.642 0.488756426 0.284 0.699 0.497 ENR+CV-2 Wbp5 Eef1g 0.641 0.470537797 0.282 0.717 0.592 ENR+CV-2 Eef1g Atp5j 0.641 0.446003672 0.282 0.805 0.692 ENR+CV-2 Atp5j Mdh2 0.639 0.620470079 0.278 0.599 0.402 ENR+CV-2 Mdh2 Myeov2 0.639 0.58079712 0.278 0.575 0.38 ENR+CV-2 Myeov2 Lars21 0.638 0.528667832 0.276 0.74 0.608 ENR+CV-2 Lars2 Mt11 0.638 0.422568466 0.276 0.835 0.656 ENR+CV-2 Mt1 Snrpg1 0.636 0.534102284 0.272 0.634 0.47 ENR+CV-2 Snrpg Cox6c1 0.636 0.365763656 0.272 0.885 0.781 ENR+CV-2 Cox6c Ldha 0.636 0.346603618 0.272 0.858 0.684 ENR+CV-2 Ldha Atp1a11 0.635 0.625292307 0.27 0.596 0.406 ENR+CV-2 Atp1a1 Trappc6a 0.632 0.713824666 0.264 0.481 0.267 ENR+CV-2 Trappc6a Tmem256 0.63 0.630557964 0.26 0.563 0.389 ENR+CV-2 Tmem256 Bsg1 0.629 0.369608482 0.258 0.823 0.731 ENR+CV-2 Bsg Crip1 0.628 0.517095126 0.256 0.605 0.4 ENR+CV-2 Crip1 Ctsb 0.627 0.575366147 0.254 0.549 0.357 ENR+CV-2 Ctsb Atp5o 0.627 0.487221882 0.254 0.67 0.534 ENR+CV-2 Atp5o Eif3h 0.627 0.453915099 0.254 0.658 0.514 ENR+CV-2 Eif3h mmu-mir-62361 0.626 1.379712556 0.252 0.295 0.053 ENR+CV-2 mmu-mir-6236 Egr11 0.626 0.580474249 0.252 0.575 0.399 ENR+CV-2 Egr1 Park7 0.626 0.537910241 0.252 0.599 0.432 ENR+CV-2 Park7 Atp5d1 0.626 0.537560089 0.252 0.593 0.424 ENR+CV-2 Atp5d Ier21 0.625 0.50775205 0.25 0.667 0.533 ENR+CV-2 Ier2 Uqcrh 0.625 0.38223009 0.25 0.752 0.644 ENR+CV-2 Uqcrh Rpl22 0.625 0.354788499 0.25 0.873 0.788 ENR+CV-2 Rpl22 Rpl3 0.625 0.321398044 0.25 0.841 0.763 ENR+CV-2 Rpl3 Hmgb1 0.624 0.668332042 0.248 0.457 0.252 ENR+CV-2 Hmgb1 Hes11 0.622 0.849232716 0.244 0.428 0.225 ENR+CV-2 Hes1 Gm9846 0.621 0.839305743 0.242 0.342 0.121 ENR+CV-2 Gm9846 Rps28 0.621 0.610513108 0.242 0.513 0.341 ENR+CV-2 Rps28 Calm11 0.621 0.291073464 0.242 0.935 0.873 ENR+CV-2 Calm1 Rps25 0.62 0.459056364 0.24 0.67 0.552 ENR+CV-2 Rps25 Uqcrc1 0.619 0.502558199 0.238 0.575 0.423 ENR+CV-2 Uqcrc1 Rny31 0.618 0.782424076 0.236 0.324 0.101 ENR+CV-2 Rny3 Ndufb4 0.618 0.665537805 0.236 0.454 0.271 ENR+CV-2 Ndufb4 Ndufc1 0.618 0.515273264 0.236 0.617 0.482 ENR+CV-2 Ndufc1 Snrpf 0.616 0.577507749 0.232 0.516 0.35 ENR+CV-2 Snrpf Snrpd3 0.616 0.517596058 0.232 0.549 0.383 ENR+CV-2 Snrpd3 Tax1bp1 0.616 0.46207462 0.232 0.617 0.465 ENR+CV-2 Tax1bp1 Serbp1 0.616 0.340116471 0.232 0.799 0.717 ENR+CV-2 Serbp1 Galk11 0.614 0.735817485 0.228 0.386 0.193 ENR+CV-2 Galk1 Ak2 0.614 0.672868468 0.228 0.463 0.288 ENR+CV-2 Ak2 Tomm7 0.614 0.440422459 0.228 0.649 0.542 ENR+CV-2 Tomm7 Rpn11 0.613 0.520693113 0.226 0.531 0.376 ENR+CV-2 Rpn1 Ndufa3 0.613 0.49423351 0.226 0.56 0.399 ENR+CV-2 Ndufa3 Cox6b1 0.612 0.306843599 0.224 0.814 0.721 ENR+CV-2 Cox6b1 Ndufs6 0.611 0.503816087 0.222 0.56 0.419 ENR+CV-2 Ndufs6 Ccdc34 0.611 0.467047338 0.222 0.59 0.428 ENR+CV-2 Ccdc34 Vim 0.609 0.744614865 0.218 0.313 0.105 ENR+CV-2 Vim Sub1 0.608 0.566390645 0.216 0.501 0.342 ENR+CV-2 Sub1 Arpp191 0.606 0.530395782 0.212 0.499 0.35 ENR+CV-2 Arpp19 Ndufv31 0.606 0.522576188 0.212 0.484 0.327 ENR+CV-2 Ndufv3 Psmc11 0.605 0.631261775 0.21 0.413 0.244 ENR+CV-2 Psmc1 Fkbp4 0.605 0.450484271 0.21 0.543 0.41 ENR+CV-2 Fkbp4 Gm10221 0.604 0.728960362 0.208 0.324 0.14 ENR+CV-2 Gm10221 Phlda1 0.604 0.574851336 0.208 0.481 0.324 ENR+CV-2 Phlda1 Rny11 0.602 0.686061504 0.204 0.286 0.09 ENR+CV-2 Rny1 Mrpl52 0.602 0.426405403 0.204 0.558 0.438 ENR+CV-2 Mrpl52 Serinc3 0.602 0.40813969 0.204 0.619 0.489 ENR+CV-2 Serinc3 Atox1 0.601 0.494023687 0.202 0.501 0.358 ENR+CV-2 Atox1 Ptma1 0.601 0.323415558 0.202 0.794 0.74 ENR+CV-2 Ptma Rpl412 0.946 1.38951703 0.892 1 0.822 ENR+CV-3 Rpl41 Pabpc12 0.932 1.115421045 0.864 1 0.797 ENR+CV-3 Pabpc1 Gm20002 0.911 1.280969343 0.822 0.982 0.436 ENR+CV-3 Gm2000 Rps18 0.901 0.82816016 0.802 1 0.918 ENR+CV-3 Rps18 Rpl37a2 0.895 1.070848195 0.79 0.991 0.584 ENR+CV-3 Rpl37a Rpl371 0.87 0.893121596 0.74 0.986 0.65 ENR+CV-3 Rpl37 Rpl35a1 0.856 0.753731854 0.712 0.995 0.782 ENR+CV-3 Rpl35a Smoc21 0.854 1.086694526 0.708 0.968 0.434 ENR+CV-3 Smoc2 Gm269242 0.853 0.662581228 0.706 1 0.935 ENR+CV-3 Gm26924 Taldo11 0.849 0.947738264 0.698 0.995 0.425 ENR+CV-3 Taldo1 Gm100761 0.838 0.827562473 0.676 0.995 0.605 ENR+CV-3 Gm10076 Bex11 0.819 1.038498168 0.638 0.882 0.271 ENR+CV-3 Bex1 Dbi2 0.818 0.645084543 0.636 1 0.818 ENR+CV-3 Dbi Uqcr101 0.816 0.743532524 0.632 0.995 0.668 ENR+CV-3 Uqcr10 Hmgcs22 0.814 1.12069006 0.628 0.738 0.095 ENR+CV-3 Hmgcs2 Ifitm21 0.811 0.801154702 0.622 0.973 0.546 ENR+CV-3 Ifitm2 Uqcr111 0.807 0.712178189 0.614 0.991 0.625 ENR+CV-3 Uqcr11 Rpl341 0.804 0.594945676 0.608 0.995 0.814 ENR+CV-3 Rpl34 Fth11 0.8 0.708081491 0.6 0.995 0.821 ENR+CV-3 Fth1 Ier22 0.796 0.856531438 0.592 0.959 0.525 ENR+CV-3 Ier2 Ndufb41 0.788 0.852050568 0.576 0.842 0.26 ENR+CV-3 Ndufb4 Cox4i11 0.784 0.511379831 0.568 1 0.852 ENR+CV-3 Cox4i1 Hsp90ab1 0.784 0.478451763 0.568 1 0.932 ENR+CV-3 Hsp90ab1 Gm155642 0.782 0.609088093 0.564 0.81 0.204 ENR+CV-3 Gm15564 Hes12 0.781 1.218509871 0.562 0.756 0.216 ENR+CV-3 Hes1 Bola22 0.778 0.799308292 0.556 0.855 0.291 ENR+CV-3 Bola2 Egr12 0.777 0.849665913 0.554 0.896 0.39 ENR+CV-3 Egr1 Atp5k1 0.772 0.661800658 0.544 0.968 0.466 ENR+CV-3 Atp5k Gm98461 0.77 0.873334033 0.54 0.674 0.112 ENR+CV-3 Gm9846 Atp5j1 0.77 0.584171958 0.54 0.991 0.687 ENR+CV-3 Atp5j H1f02 0.768 0.74386176 0.536 0.896 0.37 ENR+CV-3 H1f0 Cox6a11 0.768 0.54798628 0.536 0.995 0.7 ENR+CV-3 Cox6a1 Wbp51 0.766 0.641666207 0.532 0.968 0.491 ENR+CV-3 Wbp5 Rplp2 0.765 0.452349039 0.53 0.995 0.902 ENR+CV-3 Rplp2 Sypl 0.762 0.749466665 0.524 0.882 0.391 ENR+CV-3 Sypl Rpl141 0.759 0.430205949 0.518 1 0.922 ENR+CV-3 Rpl14 Ybx12 0.758 0.55934825 0.516 0.995 0.726 ENR+CV-3 Ybx1 Ctsb1 0.757 0.670810669 0.514 0.873 0.349 ENR+CV-3 Ctsb Aldoa1 0.754 0.666483028 0.508 0.986 0.647 ENR+CV-3 Aldoa Ak21 0.753 0.721421159 0.506 0.814 0.278 ENR+CV-3 Ak2 Myeov21 0.75 0.631872152 0.5 0.882 0.372 ENR+CV-3 Myeov2 Eif3h1 0.75 0.591732165 0.5 0.964 0.505 ENR+CV-3 Eif3h Ckb 0.749 0.682869362 0.498 0.81 0.276 ENR+CV-3 Ckb Atp1a12 0.749 0.627419723 0.498 0.914 0.397 ENR+CV-3 Atp1a1 Rps15a1 0.749 0.449087169 0.498 0.991 0.887 ENR+CV-3 Rps15a Phlda11 0.748 0.777401118 0.496 0.796 0.315 ENR+CV-3 Phlda1 Rpl131 0.748 0.417357415 0.496 0.995 0.904 ENR+CV-3 Rpl13 Mgst1 0.745 0.619861192 0.49 0.928 0.425 ENR+CV-3 Mgst1 Tmem2561 0.744 0.636439891 0.488 0.887 0.38 ENR+CV-3 Tmem256 Gm102211 0.743 0.766666364 0.486 0.638 0.132 ENR+CV-3 Gm10221 Psma71 0.743 0.538305792 0.486 0.95 0.573 ENR+CV-3 Psma7 Sub11 0.741 0.624102379 0.482 0.842 0.332 ENR+CV-3 Sub1 Cdca7 0.74 0.697599918 0.48 0.756 0.246 ENR+CV-3 Cdca7 Rps281 0.74 0.624818021 0.48 0.851 0.331 ENR+CV-3 Rps28 Rps22 0.74 0.376684404 0.48 0.995 0.933 ENR+CV-3 Rps2 Uqcrq1 0.738 0.498622019 0.476 0.991 0.755 ENR+CV-3 Uqcrq Vim1 0.737 0.954678585 0.474 0.588 0.099 ENR+CV-3 Vim Ndufb81 0.736 0.562751922 0.472 0.941 0.502 ENR+CV-3 Ndufb8 Trappc6a1 0.734 0.621645462 0.468 0.774 0.26 ENR+CV-3 Trappc6a Mlec1 0.734 0.593030871 0.468 0.864 0.356 ENR+CV-3 Mlec Cox6c2 0.734 0.454695247 0.468 1 0.779 ENR+CV-3 Cox6c Galk12 0.733 0.645641873 0.466 0.692 0.185 ENR+CV-3 Galk1 Pfdn1 0.733 0.638528383 0.466 0.742 0.231 ENR+CV-3 Pfdn1 Park71 0.733 0.567813504 0.466 0.914 0.423 ENR+CV-3 Park7 Rpl32 0.733 0.46022263 0.466 0.968 0.759 ENR+CV-3 Rpl3 Slc25a4 0.732 0.584781706 0.464 0.819 0.306 ENR+CV-3 Slc25a4 Mif1 0.732 0.568883378 0.464 0.919 0.499 ENR+CV-3 Mif Atp5e1 0.732 0.486500813 0.464 0.982 0.664 ENR+CV-3 Atp5e Mtch2 0.73 0.601281 0.46 0.81 0.3 ENR+CV-3 Mtch2 Rpl181 0.73 0.474439384 0.46 0.991 0.662 ENR+CV-3 Rpl18 Atox11 0.727 0.580173269 0.454 0.846 0.347 ENR+CV-3 Atox1 Psmc12 0.727 0.573994153 0.454 0.747 0.234 ENR+CV-3 Psmc1 2010107E04Rik1 0.727 0.487017903 0.454 0.977 0.667 ENR+CV-3 2010107E04Rik Slc25a51 0.726 0.460599637 0.452 0.995 0.761 ENR+CV-3 Slc25a5 Epcam 0.726 0.424475339 0.452 1 0.807 ENR+CV-3 Epcam Eef22 0.726 0.414431312 0.452 0.995 0.845 ENR+CV-3 Eef2 Rpl391 0.726 0.394109583 0.452 0.995 0.857 ENR+CV-3 Rpl39 Add3 0.725 0.628880588 0.45 0.701 0.211 ENR+CV-3 Add3 Eef1g1 0.725 0.512951349 0.45 0.964 0.585 ENR+CV-3 Eef1g Atp5b1 0.725 0.452478372 0.45 0.977 0.724 ENR+CV-3 Atp5b Rpl4 0.725 0.338087884 0.45 1 0.938 ENR+CV-3 Rpl4 Dynll2 0.724 0.618623907 0.448 0.751 0.267 ENR+CV-3 Dynll2 Gm4540 0.723 0.672610546 0.446 0.647 0.166 ENR+CV-3 Gm4540 Ccnd21 0.723 0.557995735 0.446 0.873 0.379 ENR+CV-3 Ccnd2 Ndufa12 0.723 0.543807321 0.446 0.842 0.347 ENR+CV-3 Ndufa12 Snord132 0.722 0.498183418 0.444 0.647 0.172 ENR+CV-3 Snord13 Cyba 0.721 0.554165323 0.442 0.701 0.205 ENR+CV-3 Cyba Ndufab1 0.721 0.520188929 0.442 0.833 0.331 ENR+CV-3 Ndufab1 Eif5a 0.721 0.500946988 0.442 0.928 0.515 ENR+CV-3 Eif5a Tomm71 0.721 0.500029484 0.442 0.946 0.533 ENR+CV-3 Tomm7 Arl3 0.719 0.69994313 0.438 0.57 0.113 ENR+CV-3 Arl3 Mdh21 0.719 0.522376731 0.438 0.855 0.396 ENR+CV-3 Mdh2 Crip11 0.719 0.506638097 0.438 0.878 0.394 ENR+CV-3 Crip1 Fuca1 0.718 0.581660075 0.436 0.697 0.22 ENR+CV-3 Fuca1 Lamp1 0.718 0.555105189 0.436 0.833 0.358 ENR+CV-3 Lamp1 Uqcrc11 0.718 0.544241079 0.436 0.882 0.414 ENR+CV-3 Uqcrc1 Snrpd31 0.718 0.538084323 0.436 0.864 0.374 ENR+CV-3 Snrpd3 Pkm2 0.718 0.509105355 0.436 0.964 0.633 ENR+CV-3 Pkm Oaz11 0.716 0.491148852 0.432 0.955 0.613 ENR+CV-3 Oaz1 Rpl351 0.716 0.442431829 0.432 0.955 0.711 ENR+CV-3 Rpl35 Hmgb11 0.715 0.644395771 0.43 0.71 0.246 ENR+CV-3 Hmgb1 Cdx1 0.715 0.551181651 0.43 0.67 0.192 ENR+CV-3 Cdx1 Snrpg2 0.715 0.542019009 0.43 0.9 0.463 ENR+CV-3 Snrpg Rny12 0.715 0.439986527 0.43 0.538 0.084 ENR+CV-3 Rny1 Csde1 0.714 0.552550741 0.428 0.801 0.309 ENR+CV-3 Csde1 Eno1 0.714 0.524899177 0.428 0.833 0.342 ENR+CV-3 Eno1 Pebp1 0.714 0.50495432 0.428 0.842 0.357 ENR+CV-3 Pebp1 Rps251 0.714 0.499252028 0.428 0.946 0.544 ENR+CV-3 Rps25 Uqcrh1 0.714 0.458430983 0.428 0.977 0.637 ENR+CV-3 Uqcrh Csnk2a1 0.713 0.642110189 0.426 0.606 0.155 ENR+CV-3 Csnk2a1 Mrpl521 0.713 0.501094602 0.426 0.91 0.427 ENR+CV-3 Mrpl52 Ndufs61 0.712 0.433312477 0.424 0.905 0.408 ENR+CV-3 Ndufs6 Calm12 0.712 0.382793703 0.424 0.991 0.872 ENR+CV-3 Calm1 Ndufs2 0.71 0.45481868 0.42 0.819 0.309 ENR+CV-3 Ndufs2 Prmt1 0.709 0.531759271 0.418 0.724 0.258 ENR+CV-3 Prmt1 Cox17 0.709 0.51590104 0.418 0.747 0.272 ENR+CV-3 Cox17 Jun 0.708 0.515651681 0.416 0.914 0.534 ENR+CV-3 Jun Arpc1b 0.707 0.551180402 0.414 0.796 0.336 ENR+CV-3 Arpc1b Tmed9 0.707 0.546826427 0.414 0.647 0.194 ENR+CV-3 Tmed9 Arpp192 0.707 0.495929126 0.414 0.819 0.34 ENR+CV-3 Arpp19 Tead2 0.706 0.621919046 0.412 0.502 0.072 ENR+CV-3 Tead2 Dsg2 0.706 0.566764688 0.412 0.638 0.189 ENR+CV-3 Dsg2 Serf2 0.706 0.552876052 0.412 0.701 0.239 ENR+CV-3 Serf2 Tmem97 0.706 0.547784866 0.412 0.697 0.24 ENR+CV-3 Tmem97 Dnajc8 0.706 0.50563781 0.412 0.724 0.251 ENR+CV-3 Dnajc8 Tpi12 0.706 0.46461955 0.412 0.955 0.583 ENR+CV-3 Tpi1 Snrpd2 0.705 0.485441588 0.41 0.851 0.387 ENR+CV-3 Snrpd2 Ndufa31 0.705 0.478980309 0.41 0.864 0.391 ENR+CV-3 Ndufa3 Ndufa5 0.705 0.465778497 0.41 0.833 0.374 ENR+CV-3 Ndufa5 Gm10269 0.703 0.50077729 0.406 0.864 0.433 ENR+CV-3 Gm10269 Ndufa1 0.703 0.489976971 0.406 0.814 0.366 ENR+CV-3 Ndufa1 Serbp11 0.703 0.39044087 0.406 0.995 0.711 ENR+CV-3 Serbp1 Ndufa10 0.702 0.508640029 0.404 0.719 0.257 ENR+CV-3 Ndufa10 Psmb3 0.702 0.499568081 0.404 0.719 0.262 ENR+CV-3 Psmb3 Comt 0.701 0.521829423 0.402 0.615 0.175 ENR+CV-3 Comt Rpn12 0.701 0.48864935 0.402 0.814 0.368 ENR+CV-3 Rpn1 Ndufc11 0.701 0.471415311 0.402 0.882 0.475 ENR+CV-3 Ndufc1 Metap2 0.7 0.457477292 0.4 0.765 0.295 ENR+CV-3 Metap2 Soat1 0.699 0.534161128 0.398 0.719 0.272 ENR+CV-3 Soat1 Atp5o1 0.699 0.465570085 0.398 0.937 0.526 ENR+CV-3 Atp5o Usmg51 0.699 0.416724209 0.398 0.955 0.595 ENR+CV-3 Usmg5 Rad23b 0.698 0.550281074 0.396 0.611 0.182 ENR+CV-3 Rad23b Idh2 0.698 0.504268037 0.396 0.674 0.231 ENR+CV-3 Idh2 Laptm4b 0.697 0.593510643 0.394 0.566 0.145 ENR+CV-3 Laptm4b Rpl17 0.697 0.501069685 0.394 0.647 0.202 ENR+CV-3 Rpl17 Cbx1 0.697 0.486674593 0.394 0.747 0.301 ENR+CV-3 Cbx1 Akr7a5 0.697 0.486341871 0.394 0.643 0.201 ENR+CV-3 Akr7a5 Ppp1r1b 0.697 0.483458592 0.394 0.719 0.27 ENR+CV-3 Ppp1r1b Acin1 0.697 0.477968862 0.394 0.756 0.301 ENR+CV-3 Acin1 Pet100 0.697 0.470323212 0.394 0.611 0.175 ENR+CV-3 Pet100 Txnip 0.697 0.452523054 0.394 0.814 0.346 ENR+CV-3 Txnip Gltscr2 0.696 0.493536009 0.392 0.729 0.289 ENR+CV-3 Gltscr2 Eml4 0.696 0.461386059 0.392 0.738 0.281 ENR+CV-3 Eml4 Ehf 0.696 0.450087744 0.392 0.783 0.319 ENR+CV-3 Ehf Hnrnpu 0.696 0.437482268 0.392 0.95 0.565 ENR+CV-3 Hnrnpu Thoc7 0.696 0.413274323 0.392 0.837 0.374 ENR+CV-3 Thoc7 Ap1s1 0.695 0.526769717 0.39 0.588 0.163 ENR+CV-3 Ap1s1 Snrpf1 0.695 0.458744027 0.39 0.801 0.342 ENR+CV-3 Snrpf Minos1 0.695 0.422558135 0.39 0.932 0.534 ENR+CV-3 Minos1 Pkig 0.694 0.564847015 0.388 0.548 0.133 ENR+CV-3 Pkig Cyp2j6 0.694 0.542500854 0.388 0.548 0.13 ENR+CV-3 Cyp2j6 Tax1bp11 0.694 0.535992833 0.388 0.837 0.459 ENR+CV-3 Tax1bp1 Apex1 0.694 0.480283271 0.388 0.62 0.185 ENR+CV-3 Apex1 Hook1 0.694 0.449640984 0.388 0.864 0.446 ENR+CV-3 Hook1 Atp6v1e1 0.694 0.41904861 0.388 0.661 0.21 ENR+CV-3 Atp6v1e1 Ndufv32 0.694 0.41551974 0.388 0.796 0.318 ENR+CV-3 Ndufv3 Dnaja1 0.693 0.472692722 0.386 0.629 0.194 ENR+CV-3 Dnaja1 Aprt 0.693 0.435115211 0.386 0.738 0.279 ENR+CV-3 Aprt Sord 0.692 0.557387596 0.384 0.611 0.192 ENR+CV-3 Sord Acat1 0.692 0.553756071 0.384 0.566 0.151 ENR+CV-3 Acat1 Wdr43 0.692 0.530751722 0.384 0.624 0.201 ENR+CV-3 Wdr43 Tmed2 0.692 0.481892892 0.384 0.624 0.194 ENR+CV-3 Tmed2 Aldh9a11 0.692 0.481803816 0.384 0.602 0.173 ENR+CV-3 Aldh9a1 Arpc5 0.692 0.430571372 0.384 0.774 0.313 ENR+CV-3 Arpc5 1110004F10Rik 0.691 0.48303973 0.382 0.638 0.208 ENR+CV-3 1110004F10Rik Spcs2 0.691 0.427443596 0.382 0.819 0.371 ENR+CV-3 Spcs2 Oat 0.69 0.485645315 0.38 0.824 0.405 ENR+CV-3 Oat Snw1 0.69 0.478948898 0.38 0.665 0.237 ENR+CV-3 Snw1 2410015M20Rik1 0.69 0.470502234 0.38 0.683 0.245 ENR+CV-3 2410015M20Rik Mrpl33 0.69 0.433850397 0.38 0.828 0.379 ENR+CV-3 Mrpl33 Junb1 0.689 0.573703823 0.378 0.76 0.379 ENR+CV-3 Junb Axin2 0.689 0.524359624 0.378 0.643 0.228 ENR+CV-3 Axin2 Mfge8 0.689 0.49247588 0.378 0.597 0.173 ENR+CV-3 Mfge8 Lamtor2 0.689 0.475494943 0.378 0.615 0.193 ENR+CV-3 Lamtor2 Lima1 0.689 0.45266264 0.378 0.679 0.244 ENR+CV-3 Lima1 Ubqln1 0.688 0.534669301 0.376 0.584 0.178 ENR+CV-3 Ubqln1 Psmc3 0.688 0.524369149 0.376 0.643 0.225 ENR+CV-3 Psmc3 Lad1 0.688 0.514307509 0.376 0.629 0.213 ENR+CV-3 Lad1 Uchl3 0.688 0.500086828 0.376 0.557 0.144 ENR+CV-3 Uchl3 Mapk131 0.688 0.493697597 0.376 0.647 0.222 ENR+CV-3 Mapk13 0610011F06Rik 0.688 0.485923426 0.376 0.606 0.192 ENR+CV-3 0610011F06Rik Tecr 0.688 0.474383501 0.376 0.783 0.342 ENR+CV-3 Tecr Sars 0.688 0.417812344 0.376 0.742 0.296 ENR+CV-3 Sars Fgfbp1 0.687 0.493895446 0.374 0.656 0.235 ENR+CV-3 Fgfbp1 Tmem160 0.687 0.47622251 0.374 0.624 0.203 ENR+CV-3 Tmem160 Tubb51 0.687 0.375347083 0.374 0.982 0.584 ENR+CV-3 Tubb5 Gsk3b 0.686 0.500189713 0.372 0.566 0.159 ENR+CV-3 Gsk3b App 0.686 0.471694593 0.372 0.783 0.348 ENR+CV-3 App Cd9 0.686 0.427843824 0.372 0.679 0.247 ENR+CV-3 Cd9 Dnase2a 0.685 0.613718118 0.37 0.511 0.12 ENR+CV-3 Dnase2a Rpl36 0.685 0.481849544 0.37 0.561 0.156 ENR+CV-3 Rpl36 Cldn7 0.685 0.432196745 0.37 0.946 0.605 ENR+CV-3 Cldn7 Hsd17b10 0.685 0.42841952 0.37 0.62 0.199 ENR+CV-3 Hsd17b10 Cyb5b 0.685 0.398828102 0.37 0.679 0.238 ENR+CV-3 Cyb5b Eif3e 0.685 0.385606147 0.37 0.824 0.363 ENR+CV-3 Eif3e Idh3a 0.684 0.456073175 0.368 0.633 0.214 ENR+CV-3 Idh3a Ndufb7 0.684 0.427776183 0.368 0.756 0.32 ENR+CV-3 Ndufb7 Bzw1 0.684 0.426022225 0.368 0.796 0.37 ENR+CV-3 Bzw1 Mrpl12 0.684 0.419145279 0.368 0.769 0.327 ENR+CV-3 Mrpl12 Glrx 0.683 0.52357108 0.366 0.538 0.144 ENR+CV-3 Glrx Ctsa 0.683 0.47825754 0.366 0.557 0.154 ENR+CV-3 Ctsa Pcsk91 0.683 0.469291573 0.366 0.566 0.161 ENR+CV-3 Pcsk9 Mvb12a 0.683 0.454207468 0.366 0.548 0.145 ENR+CV-3 Mvb12a Arpc2 0.683 0.422174137 0.366 0.851 0.426 ENR+CV-3 Arpc2 Bzw2 0.683 0.421530304 0.366 0.719 0.289 ENR+CV-3 Bzw2 Atp5d2 0.683 0.414779573 0.366 0.873 0.417 ENR+CV-3 Atp5d Ndufa61 0.683 0.340849804 0.366 0.977 0.718 ENR+CV-3 Ndufa6 Rpl221 0.683 0.322613878 0.366 0.991 0.785 ENR+CV-3 Rpl22 Acot11 0.682 0.614570561 0.364 0.471 0.092 ENR+CV-3 Acot1 Pdcd10 0.682 0.438298087 0.364 0.548 0.145 ENR+CV-3 Pdcd10 Suclg1 0.682 0.416695547 0.364 0.76 0.334 ENR+CV-3 Suclg1 Cops6 0.682 0.409094336 0.364 0.674 0.238 ENR+CV-3 Cops6 Mdh1 0.682 0.387172038 0.364 0.819 0.367 ENR+CV-3 Mdh1 Znhit1 0.681 0.524642877 0.362 0.529 0.139 ENR+CV-3 Znhit1 Pabpc41 0.681 0.521062663 0.362 0.566 0.175 ENR+CV-3 Pabpc4 Lta4h 0.681 0.50672711 0.362 0.57 0.176 ENR+CV-3 Lta4h Ywhab 0.681 0.399289516 0.362 0.76 0.32 ENR+CV-3 Ywhab Gsta4 0.681 0.389742797 0.362 0.661 0.231 ENR+CV-3 Gsta4 Aqp11 0.68 0.557672201 0.36 0.534 0.149 ENR+CV-3 Aqp1 Arhgef26 0.68 0.548666846 0.36 0.529 0.144 ENR+CV-3 Arhgef26 H2-Q101 0.68 0.52104614 0.36 0.507 0.121 ENR+CV-3 H2-Q10 Twf1 0.68 0.439306173 0.36 0.67 0.252 ENR+CV-3 Twf1 Nme1 0.68 0.387850695 0.36 0.923 0.559 ENR+CV-3 Nme1 Cope 0.68 0.374611929 0.36 0.747 0.306 ENR+CV-3 Cope Zfp36 0.679 0.543233338 0.358 0.593 0.204 ENR+CV-3 Zfp36 Hmg20b 0.679 0.53467553 0.358 0.566 0.177 ENR+CV-3 Hmg20b Dcun1d5 0.679 0.486130114 0.358 0.548 0.158 ENR+CV-3 Dcun1d5 Psmb2 0.679 0.433742397 0.358 0.665 0.25 ENR+CV-3 Psmb2 Pls1 0.679 0.423596256 0.358 0.593 0.189 ENR+CV-3 Pls1 Hopx 0.679 0.409355664 0.358 0.742 0.305 ENR+CV-3 Hopx Chchd10 0.679 0.408157904 0.358 0.742 0.309 ENR+CV-3 Chchd10 Dad1 0.679 0.381908568 0.358 0.769 0.331 ENR+CV-3 Dad1 Canx 0.679 0.380533037 0.358 0.891 0.499 ENR+CV-3 Canx Aldh2 0.678 0.4639208 0.356 0.552 0.161 ENR+CV-3 Aldh2 Sox41 0.678 0.4392346 0.356 0.783 0.366 ENR+CV-3 Sox4 Ywhaz 0.678 0.400032937 0.356 0.805 0.376 ENR+CV-3 Ywhaz H2afv 0.678 0.37940599 0.356 0.828 0.387 ENR+CV-3 H2afv G3bp1 0.678 0.37671642 0.356 0.729 0.287 ENR+CV-3 G3bp1 Sfxn1 0.677 0.441768707 0.354 0.575 0.182 ENR+CV-3 Sfxn1 Ctsz 0.677 0.430988794 0.354 0.611 0.208 ENR+CV-3 Ctsz Eif4a1 0.677 0.385100864 0.354 0.905 0.476 ENR+CV-3 Eif4a1 Ndufb2 0.677 0.364182611 0.354 0.828 0.388 ENR+CV-3 Ndufb2 Bex4 0.676 0.545701687 0.352 0.443 0.076 ENR+CV-3 Bex4 Bri3 0.676 0.452087739 0.352 0.557 0.168 ENR+CV-3 Bri3 Serinc31 0.676 0.420862488 0.352 0.864 0.483 ENR+CV-3 Serinc3 Cers6 0.676 0.395466968 0.352 0.638 0.227 ENR+CV-3 Cers6 Eif3f 0.676 0.386926285 0.352 0.864 0.429 ENR+CV-3 Eif3f Srrm1 0.676 0.37766384 0.352 0.751 0.331 ENR+CV-3 Srrm1 1110001J03Rik 0.676 0.363553813 0.352 0.633 0.218 ENR+CV-3 1110001J03Rik Rpl8 0.676 0.260214241 0.352 1 0.923 ENR+CV-3 Rpl8 mt-Tc1 0.675 0.639123219 0.35 0.421 0.061 ENR+CV-3 mt-Tc Cps1 0.675 0.426588497 0.35 0.765 0.354 ENR+CV-3 Cps1 1500012F01Rik 0.675 0.406799037 0.35 0.937 0.572 ENR+CV-3 1500012F01Rik Cacybp 0.675 0.366274181 0.35 0.719 0.295 ENR+CV-3 Cacybp Clybl 0.674 0.611557978 0.348 0.434 0.073 ENR+CV-3 Clybl Rpl7l1 0.674 0.492337758 0.348 0.552 0.174 ENR+CV-3 Rpl7l1 Rny32 0.674 0.470854807 0.348 0.471 0.1 ENR+CV-3 Rny3 Cbx3 0.674 0.469049363 0.348 0.529 0.15 ENR+CV-3 Cbx3 Aifm1 0.674 0.444019111 0.348 0.525 0.145 ENR+CV-3 Aifm1 Nsun2 0.674 0.436448825 0.348 0.602 0.211 ENR+CV-3 Nsun2 Ppp1ca 0.674 0.382771358 0.348 0.824 0.399 ENR+CV-3 Ppp1ca Lamp2 0.674 0.368635373 0.348 0.719 0.288 ENR+CV-3 Lamp2 Tkt1 0.674 0.358386366 0.348 0.878 0.456 ENR+CV-3 Tkt Selm 0.674 0.358159816 0.348 0.674 0.241 ENR+CV-3 Selm Mrpl15 0.674 0.347372791 0.348 0.692 0.268 ENR+CV-3 Mrpl15 Nrtn 0.673 0.53091795 0.346 0.439 0.079 ENR+CV-3 Nrtn Clptm1 0.673 0.469160678 0.346 0.507 0.135 ENR+CV-3 Clptm1 Tspo 0.673 0.46243975 0.346 0.534 0.156 ENR+CV-3 Tspo Cct7 0.673 0.409761799 0.346 0.729 0.319 ENR+CV-3 Cct7 Tbca 0.673 0.380328447 0.346 0.719 0.311 ENR+CV-3 Tbca Sptssa 0.673 0.37717076 0.346 0.715 0.298 ENR+CV-3 Sptssa Rbm8a 0.673 0.376574226 0.346 0.62 0.216 ENR+CV-3 Rbm8a Ndufa41 0.673 0.32906803 0.346 0.977 0.748 ENR+CV-3 Ndufa4 Ndufs5 0.672 0.500986975 0.344 0.498 0.129 ENR+CV-3 Ndufs5 Sdhc 0.672 0.426909918 0.344 0.611 0.219 ENR+CV-3 Sdhc Pdha1 0.672 0.416285807 0.344 0.674 0.27 ENR+CV-3 Pdha1 Anp32a 0.672 0.404571369 0.344 0.787 0.372 ENR+CV-3 Anp32a Eif4e2 0.672 0.40339984 0.344 0.557 0.17 ENR+CV-3 Eif4e2 Etfb 0.672 0.349009015 0.344 0.805 0.374 ENR+CV-3 Etfb Cox6b11 0.672 0.317394065 0.344 0.977 0.717 ENR+CV-3 Cox6b1 Phb 0.671 0.507311685 0.342 0.502 0.136 ENR+CV-3 Phb Rgcc 0.671 0.440443985 0.342 0.747 0.366 ENR+CV-3 Rgcc Ggh 0.671 0.382163233 0.342 0.525 0.147 ENR+CV-3 Ggh Nol7 0.671 0.377761019 0.342 0.738 0.325 ENR+CV-3 Nol7 Psmb5 0.671 0.340881727 0.342 0.656 0.244 ENR+CV-3 Psmb5 Rab14 0.67 0.420691706 0.34 0.548 0.17 ENR+CV-3 Rab14 Cdc37 0.67 0.352091696 0.34 0.665 0.257 ENR+CV-3 Cdc37 Tmem234 0.67 0.338674832 0.34 0.679 0.265 ENR+CV-3 Tmem234 Ndufs4 0.67 0.279670847 0.34 0.751 0.311 ENR+CV-3 Ndufs4 Sec31a 0.669 0.448918499 0.338 0.543 0.171 ENR+CV-3 Sec31a Ubc1 0.669 0.431980907 0.338 0.887 0.56 ENR+CV-3 Ubc Ugp2 0.669 0.411997002 0.338 0.538 0.165 ENR+CV-3 Ugp2 Psap 0.669 0.382956096 0.338 0.579 0.193 ENR+CV-3 Psap Mtdh 0.669 0.376522728 0.338 0.706 0.307 ENR+CV-3 Mtdh Cox7c 0.669 0.363624068 0.338 0.774 0.36 ENR+CV-3 Cox7c Hbegf 0.668 0.557694397 0.336 0.575 0.211 ENR+CV-3 Hbegf Rgmb 0.668 0.551997456 0.336 0.471 0.117 ENR+CV-3 Rgmb Anapc13 0.668 0.385261924 0.336 0.674 0.285 ENR+CV-3 Anapc13 Eif1 0.668 0.381477039 0.336 0.837 0.429 ENR+CV-3 Eif1 Aldh1b1 0.668 0.377830257 0.336 0.756 0.341 ENR+CV-3 Aldh1b1 Cyc1 0.668 0.344214435 0.336 0.765 0.333 ENR+CV-3 Cyc1 Rpl11 0.668 0.329616289 0.336 0.692 0.274 ENR+CV-3 Rpl11 Agpat5 0.667 0.463994026 0.334 0.507 0.146 ENR+CV-3 Agpat5 Mrps9 0.667 0.421553246 0.334 0.475 0.115 ENR+CV-3 Mrps9 Dhcr241 0.667 0.419815518 0.334 0.593 0.215 ENR+CV-3 Dhcr24 M6pr 0.667 0.418331301 0.334 0.538 0.169 ENR+CV-3 M6pr Lsmd1 0.667 0.417065804 0.334 0.606 0.227 ENR+CV-3 Lsmd1 Rnf43 0.667 0.402866103 0.334 0.557 0.179 ENR+CV-3 Rnf43 Romo1 0.667 0.384855022 0.334 0.787 0.388 ENR+CV-3 Romo1 G3bp2 0.667 0.381242612 0.334 0.624 0.235 ENR+CV-3 G3bp2 Cs1 0.667 0.375513523 0.334 0.629 0.235 ENR+CV-3 Cs Rpl31 0.667 0.36337708 0.334 0.747 0.336 ENR+CV-3 Rpl31 Tma7 0.667 0.356008977 0.334 0.62 0.228 ENR+CV-3 Tma7 Dhrs4 0.667 0.355896436 0.334 0.606 0.214 ENR+CV-3 Dhrs4 Rars 0.667 0.34475371 0.334 0.688 0.283 ENR+CV-3 Rars Mrpl28 0.667 0.31968058 0.334 0.656 0.247 ENR+CV-3 Mrpl28 2810004N23Rik 0.666 0.444384453 0.332 0.516 0.154 ENR+CV-3 2810004N23Rik Psmd12 0.666 0.402564136 0.332 0.561 0.189 ENR+CV-3 Psmd12 Gstm5 0.666 0.388455782 0.332 0.611 0.23 ENR+CV-3 Gstm5 Cox5a 0.666 0.349363164 0.332 0.873 0.471 ENR+CV-3 Cox5a Tmem9 0.665 0.490674293 0.33 0.443 0.096 ENR+CV-3 Tmem9 Bax 0.665 0.394924644 0.33 0.624 0.242 ENR+CV-3 Bax 1-Sep 0.665 0.357230826 0.33 0.611 0.226 ENR+CV-3 1-Sep H3f3b 0.665 0.340444196 0.33 0.982 0.723 ENR+CV-3 H3f3b Dhx15 0.665 0.327910415 0.33 0.665 0.262 ENR+CV-3 Dhx15 Slc30a2 0.664 0.604270773 0.328 0.403 0.066 ENR+CV-3 Slc30a2 Tspan3 0.664 0.33623694 0.328 0.656 0.26 ENR+CV-3 Tspan3 Ube2d3 0.664 0.324640178 0.328 0.724 0.309 ENR+CV-3 Ube2d3 Hdac1 0.663 0.481607952 0.326 0.507 0.154 ENR+CV-3 Hdac1 Nipsnap1 0.663 0.457181968 0.326 0.48 0.129 ENR+CV-3 Nipsnap1 Zfp36l1 0.663 0.420553912 0.326 0.588 0.219 ENR+CV-3 Zfp36l1 Capzb 0.663 0.363835893 0.326 0.67 0.278 ENR+CV-3 Capzb Wdr61 0.663 0.360212059 0.326 0.584 0.207 ENR+CV-3 Wdr61 Pla2g12a 0.662 0.424855263 0.324 0.475 0.125 ENR+CV-3 Pla2g12a Cox19 0.662 0.405330027 0.324 0.466 0.116 ENR+CV-3 Cox19 Itga6 0.662 0.395628914 0.324 0.525 0.162 ENR+CV-3 Itga6 Map1lc3b 0.662 0.372603853 0.324 0.561 0.194 ENR+CV-3 Map1lc3b Snrnp27 0.662 0.36980055 0.324 0.529 0.164 ENR+CV-3 Snrnp27 Pdap11 0.662 0.363650304 0.324 0.814 0.401 ENR+CV-3 Pdap1 Pfdn5 0.662 0.337866101 0.324 0.851 0.434 ENR+CV-3 Pfdn5 Nop56 0.662 0.332577331 0.324 0.715 0.308 ENR+CV-3 Nop56 Ngfrap1 0.662 0.318460504 0.324 0.584 0.197 ENR+CV-3 Ngfrap1 Rabac1 0.661 0.382964087 0.322 0.534 0.173 ENR+CV-3 Rabac1 Psmd4 0.661 0.379567113 0.322 0.588 0.218 ENR+CV-3 Psmd4 Hadh 0.661 0.356440385 0.322 0.706 0.31 ENR+CV-3 Hadh Atxn7l3b 0.661 0.310746992 0.322 0.697 0.301 ENR+CV-3 Atxn7l3b Eif3k 0.661 0.281320925 0.322 0.828 0.393 ENR+CV-3 Eif3k Sec61a1 0.661 0.271179249 0.322 0.643 0.239 ENR+CV-3 Sec61a1 Ide 0.66 0.488756057 0.32 0.439 0.102 ENR+CV-3 Ide Mrpl19 0.66 0.413515979 0.32 0.452 0.11 ENR+CV-3 Mrpl19 Ndufaf2 0.66 0.394393121 0.32 0.534 0.176 ENR+CV-3 Ndufaf2 Eif4g1 0.66 0.367880563 0.32 0.778 0.389 ENR+CV-3 Eif4g1 Ndufa11 0.66 0.326364143 0.32 0.688 0.299 ENR+CV-3 Ndufa11 Hsbp1 0.66 0.323790398 0.32 0.692 0.303 ENR+CV-3 Hsbp1 Mrps12 0.659 0.465508517 0.318 0.493 0.149 ENR+CV-3 Mrps12 Vps29 0.659 0.430839301 0.318 0.552 0.199 ENR+CV-3 Vps29 Psmd11 0.659 0.413800457 0.318 0.511 0.162 ENR+CV-3 Psmd11 Mybbp1a 0.659 0.378988338 0.318 0.593 0.224 ENR+CV-3 Mybbp1a Rpn2 0.659 0.366068839 0.318 0.674 0.282 ENR+CV-3 Rpn2 Naa50 0.659 0.355733005 0.318 0.588 0.215 ENR+CV-3 Naa50 Mbnl1 0.659 0.324920647 0.318 0.566 0.194 ENR+CV-3 Mbnl1 Hnrnpc 0.659 0.297096126 0.318 0.778 0.364 ENR+CV-3 Hnrnpc Rpl23 0.659 0.291269289 0.318 0.977 0.738 ENR+CV-3 Rpl23 Fbln1 0.658 0.586105927 0.316 0.407 0.082 ENR+CV-3 Fbln1 Tsc22d4 0.658 0.495217738 0.316 0.434 0.102 ENR+CV-3 Tsc22d4 Mrps5 0.658 0.428060518 0.316 0.48 0.138 ENR+CV-3 Mrps5 Acaa2 0.658 0.400591759 0.316 0.543 0.192 ENR+CV-3 Acaa2 Set 0.658 0.345662177 0.316 0.778 0.369 ENR+CV-3 Set Fkbp41 0.658 0.333120081 0.316 0.805 0.403 ENR+CV-3 Fkbp4 Atp1b1 0.658 0.329673354 0.316 0.946 0.603 ENR+CV-3 Atp1b1 Echs1 0.658 0.321404678 0.316 0.647 0.262 ENR+CV-3 Echs1 Sec61b1 0.658 0.319870671 0.316 0.941 0.586 ENR+CV-3 Sec61b Ccdc341 0.658 0.309400549 0.316 0.824 0.422 ENR+CV-3 Ccdc34 Rsl1d1 0.658 0.264753373 0.316 0.846 0.412 ENR+CV-3 Rsl1d1 Blvrb 0.657 0.52375726 0.314 0.412 0.083 ENR+CV-3 Blvrb Utp14a 0.657 0.43647759 0.314 0.471 0.132 ENR+CV-3 Utp14a Sec61g 0.657 0.368221777 0.314 0.52 0.166 ENR+CV-3 Sec61g Vps36 0.657 0.355144395 0.314 0.529 0.175 ENR+CV-3 Vps36 Timm8b 0.657 0.330304073 0.314 0.747 0.36 ENR+CV-3 Timm8b Eif1a 0.657 0.318393238 0.314 0.606 0.23 ENR+CV-3 Eif1a Ctsd 0.657 0.28821548 0.314 0.624 0.241 ENR+CV-3 Ctsd Hdac3 0.656 0.378849022 0.312 0.466 0.126 ENR+CV-3 Hdac3 Slc25a11 0.656 0.368217853 0.312 0.552 0.196 ENR+CV-3 Slc25a1 Psmd7 0.656 0.343184176 0.312 0.602 0.238 ENR+CV-3 Psmd7 Ndufs8 0.656 0.338336758 0.312 0.706 0.337 ENR+CV-3 Ndufs8 Rp9 0.656 0.312939772 0.312 0.584 0.216 ENR+CV-3 Rp9 Psmb1 0.656 0.309764773 0.312 0.937 0.592 ENR+CV-3 Psmb1 Cox7b1 0.656 0.262152249 0.312 0.982 0.718 ENR+CV-3 Cox7b Got2 0.655 0.450646661 0.31 0.462 0.129 ENR+CV-3 Got2 Cdx2 0.655 0.435416547 0.31 0.452 0.122 ENR+CV-3 Cdx2 Hnrnpd 0.655 0.432673927 0.31 0.507 0.17 ENR+CV-3 Hnrnpd Rps6ka1 0.655 0.367238198 0.31 0.484 0.143 ENR+CV-3 Rps6ka1 Tuba1a 0.655 0.355001098 0.31 0.575 0.209 ENR+CV-3 Tuba1a D8Ertd738e 0.655 0.314709962 0.31 0.593 0.224 ENR+CV-3 D8Ertd738e Tmed10 0.655 0.287977245 0.31 0.615 0.24 ENR+CV-3 Tmed10 1700021F05Rik 0.654 0.43773033 0.308 0.412 0.086 ENR+CV-3 1700021F05Rik Glrx5 0.654 0.408510597 0.308 0.475 0.139 ENR+CV-3 Glrx5 Tmco1 0.654 0.360663004 0.308 0.548 0.195 ENR+CV-3 Tmco1 Calm3 0.654 0.333689293 0.308 0.683 0.302 ENR+CV-3 Calm3 Hnf4a 0.654 0.329935812 0.308 0.602 0.236 ENR+CV-3 Hnf4a Ubb1 0.654 0.317064389 0.308 0.95 0.736 ENR+CV-3 Ubb Nedd8 0.654 0.312957903 0.308 0.76 0.368 ENR+CV-3 Nedd8 Eif5b 0.654 0.310991506 0.308 0.724 0.332 ENR+CV-3 Eif5b Cnn3 0.654 0.307853601 0.308 0.597 0.228 ENR+CV-3 Cnn3 Eif3g 0.654 0.295226771 0.308 0.67 0.283 ENR+CV-3 Eif3g Ssx2ip 0.653 0.521029014 0.306 0.407 0.091 ENR+CV-3 Ssx2ip Nlrp6 0.653 0.416098058 0.306 0.493 0.154 ENR+CV-3 Nlrp6 Serinc2 0.653 0.398049586 0.306 0.502 0.163 ENR+CV-3 Serinc2 Ppa2 0.653 0.379126938 0.306 0.489 0.151 ENR+CV-3 Ppa2 Mrpl46 0.653 0.359344953 0.306 0.48 0.142 ENR+CV-3 Mrpl46 Gstm1 0.653 0.355427205 0.306 0.543 0.196 ENR+CV-3 Gstm1 Hnrnpm 0.653 0.351476052 0.306 0.665 0.307 ENR+CV-3 Hnrnpm Creg1 0.653 0.345693685 0.306 0.529 0.18 ENR+CV-3 Creg1 Cdc123 0.653 0.340527625 0.306 0.543 0.193 ENR+CV-3 Cdc123 Fam96a 0.653 0.331605712 0.306 0.566 0.207 ENR+CV-3 Fam96a Grpel1 0.653 0.330019138 0.306 0.57 0.213 ENR+CV-3 Grpel1 Rrp1 0.653 0.32387393 0.306 0.606 0.244 ENR+CV-3 Rrp1 Arf1 0.653 0.319639847 0.306 0.715 0.333 ENR+CV-3 Arf1 Glrx3 0.653 0.31778968 0.306 0.643 0.271 ENR+CV-3 Glrx3 Txn2 0.653 0.30125191 0.306 0.624 0.25 ENR+CV-3 Txn2 Sdhb 0.653 0.274872548 0.306 0.796 0.385 ENR+CV-3 Sdhb Slc16a31 0.652 0.552984854 0.304 0.421 0.104 ENR+CV-3 Slc16a3 Aqp4 0.652 0.430300806 0.304 0.439 0.114 ENR+CV-3 Aqp4 Mecr 0.652 0.424678617 0.304 0.412 0.091 ENR+CV-3 Mecr Smarcd2 0.652 0.416444849 0.304 0.434 0.108 ENR+CV-3 Smarcd2 Rab3d 0.652 0.411728795 0.304 0.457 0.128 ENR+CV-3 Rab3d Elf31 0.652 0.40681823 0.304 0.643 0.293 ENR+CV-3 Elf3 Lamtor5 0.652 0.341273367 0.304 0.475 0.139 ENR+CV-3 Lamtor5 Golm1 0.652 0.320971197 0.304 0.507 0.162 ENR+CV-3 Golm1 Copz1 0.652 0.313980132 0.304 0.543 0.189 ENR+CV-3 Copz1 Cox5b 0.652 0.305534058 0.304 0.846 0.433 ENR+CV-3 Cox5b Eif3b 0.652 0.300546197 0.304 0.548 0.191 ENR+CV-3 Eif3b Psmb4 0.652 0.300465821 0.304 0.719 0.325 ENR+CV-3 Psmb4 Pisd 0.651 0.395463229 0.302 0.457 0.13 ENR+CV-3 Pisd Ubxn2a 0.651 0.388763849 0.302 0.443 0.119 ENR+CV-3 Ubxn2a Smarcc1 0.651 0.324418825 0.302 0.579 0.224 ENR+CV-3 Smarcc1 Amica1 0.65 0.350100595 0.3 0.615 0.264 ENR+CV-3 Amica1 Slc38a2 0.65 0.346975256 0.3 0.548 0.204 ENR+CV-3 Slc38a2 Hsd17b12 0.65 0.29507241 0.3 0.624 0.254 ENR+CV-3 Hsd17b12 Ptma2 0.65 0.293587788 0.3 0.959 0.735 ENR+CV-3 Ptma Tomm70a 0.65 0.280206151 0.3 0.615 0.249 ENR+CV-3 Tomm70a Xrn2 0.65 0.277571574 0.3 0.62 0.26 ENR+CV-3 Xrn2 Stip1 0.65 0.275127738 0.3 0.629 0.257 ENR+CV-3 Stip1 Cap1 0.649 0.392687434 0.298 0.475 0.15 ENR+CV-3 Cap1 Sumo3 0.649 0.386685597 0.298 0.48 0.152 ENR+CV-3 Sumo3 Sumo1 0.649 0.342421649 0.298 0.561 0.215 ENR+CV-3 Sumo1 Pomp 0.649 0.336108489 0.298 0.706 0.338 ENR+CV-3 Pomp Zranb2 0.649 0.334525165 0.298 0.516 0.179 ENR+CV-3 Zranb2 Cpne3 0.649 0.328110325 0.298 0.52 0.183 ENR+CV-3 Cpne3 D17Wsu104e 0.649 0.327585136 0.298 0.566 0.217 ENR+CV-3 D17Wsu104e Ppp1cb 0.649 0.314287032 0.298 0.579 0.227 ENR+CV-3 Ppp1cb Glo1 0.649 0.313039606 0.298 0.502 0.164 ENR+CV-3 Glo1 Tomm22 0.649 0.312294276 0.298 0.633 0.278 ENR+CV-3 Tomm22 Ndufv1 0.649 0.304765319 0.298 0.593 0.234 ENR+CV-3 Ndufv1 Wdr891 0.649 0.295565578 0.298 0.882 0.527 ENR+CV-3 Wdr89 Eif3c 0.649 0.271873036 0.298 0.842 0.445 ENR+CV-3 Eif3c Ass1 0.648 0.506817715 0.296 0.344 0.042 ENR+CV-3 Ass1 mmu-mir-62362 0.648 0.369307757 0.296 0.362 0.055 ENR+CV-3 mmu-mir-6236 Stt3b 0.648 0.346988483 0.296 0.525 0.191 ENR+CV-3 Stt3b Ccdc107 0.648 0.316305859 0.296 0.48 0.146 ENR+CV-3 Ccdc107 Hnrnpk1 0.648 0.308928821 0.296 0.855 0.495 ENR+CV-3 Hnrnpk Ddost 0.648 0.291953994 0.296 0.683 0.304 ENR+CV-3 Ddost Eif1ax 0.648 0.267122284 0.296 0.606 0.243 ENR+CV-3 Eif1ax Cct2 0.648 0.256968702 0.296 0.824 0.409 ENR+CV-3 Cct2 Prelid2 0.647 0.411835492 0.294 0.439 0.121 ENR+CV-3 Prelid2 Rtcb 0.647 0.388380605 0.294 0.484 0.159 ENR+CV-3 Rtcb U2af1 0.647 0.377912896 0.294 0.475 0.151 ENR+CV-3 U2af1 Snrpb2 0.647 0.375695413 0.294 0.484 0.158 ENR+CV-3 Snrpb2 Strbp 0.647 0.357229211 0.294 0.511 0.182 ENR+CV-3 Strbp Cftr 0.647 0.354386892 0.294 0.466 0.141 ENR+CV-3 Cftr Aldh18a1 0.647 0.344465858 0.294 0.48 0.152 ENR+CV-3 Aldh18a1 Dnm1l 0.647 0.311371794 0.294 0.52 0.182 ENR+CV-3 Dnm1l Immt 0.647 0.298640382 0.294 0.584 0.234 ENR+CV-3 Immt Myl12b 0.647 0.275917313 0.294 0.837 0.452 ENR+CV-3 Myl12b Psmc4 0.646 0.364910255 0.292 0.516 0.185 ENR+CV-3 Psmc4 Dap3 0.646 0.326528683 0.292 0.52 0.188 ENR+CV-3 Dap3 Usp10 0.646 0.325921398 0.292 0.452 0.129 ENR+CV-3 Usp10 Gale 0.646 0.313605258 0.292 0.502 0.167 ENR+CV-3 Gale Ier3ip1 0.646 0.305174497 0.292 0.548 0.207 ENR+CV-3 Ier3ip1 Nap1l4 0.646 0.303317978 0.292 0.552 0.21 ENR+CV-3 Nap1l4 Gnb2 0.646 0.295638501 0.292 0.719 0.343 ENR+CV-3 Gnb2 Fam162a 0.646 0.295326161 0.292 0.715 0.347 ENR+CV-3 Fam162a Gm10036 0.646 0.279939182 0.292 0.665 0.292 ENR+CV-3 Gm10036 Bnip3 0.645 0.393338347 0.29 0.484 0.165 ENR+CV-3 Bnip3 Uri1 0.645 0.341193804 0.29 0.448 0.131 ENR+CV-3 Uri1 Dctpp1 0.645 0.334637826 0.29 0.529 0.194 ENR+CV-3 Dctpp1 Tmem50a 0.645 0.334286511 0.29 0.489 0.165 ENR+CV-3 Tmem50a Ccnd1 0.645 0.326635361 0.29 0.516 0.184 ENR+CV-3 Ccnd1 1110008F13Rik 0.645 0.310849832 0.29 0.606 0.258 ENR+CV-3 1110008F13Rik Denr 0.645 0.305628743 0.29 0.529 0.194 ENR+CV-3 Denr Bsg2 0.645 0.305584942 0.29 0.977 0.727 ENR+CV-3 Bsg Tceb1 0.645 0.292599058 0.29 0.652 0.293 ENR+CV-3 Tceb1 Impa1 0.645 0.285801929 0.29 0.502 0.169 ENR+CV-3 Impa1 Hnrnpl 0.645 0.278111231 0.29 0.633 0.271 ENR+CV-3 Hnrnpl Acot7 0.644 0.458173346 0.288 0.385 0.084 ENR+CV-3 Acot7 Cdkn2aipnl 0.644 0.395076573 0.288 0.421 0.112 ENR+CV-3 Cdkn2aipnl Cggbp1 0.644 0.386049236 0.288 0.48 0.161 ENR+CV-3 Cggbp1 Ipo7 0.644 0.380692032 0.288 0.448 0.135 ENR+CV-3 Ipo7 Dctn3 0.644 0.368267225 0.288 0.462 0.145 ENR+CV-3 Dctn3 Ptgr1 0.644 0.365445714 0.288 0.552 0.226 ENR+CV-3 Ptgr1 Drap1 0.644 0.353677705 0.288 0.466 0.148 ENR+CV-3 Drap1 Acadl 0.644 0.348704738 0.288 0.434 0.121 ENR+CV-3 Acadl Carhsp1 0.644 0.345915621 0.288 0.462 0.141 ENR+CV-3 Carhsp1 Lpcat3 0.644 0.339806156 0.288 0.466 0.146 ENR+CV-3 Lpcat3 Pcbp2 0.644 0.322415443 0.288 0.765 0.392 ENR+CV-3 Pcbp2 H2-D1 0.644 0.316236466 0.288 0.729 0.365 ENR+CV-3 H2-D1 Ghitm 0.644 0.300525729 0.288 0.71 0.345 ENR+CV-3 Ghitm Abcf1 0.644 0.292064404 0.288 0.588 0.24 ENR+CV-3 Abcf1 Ldha1 0.644 0.272884837 0.288 0.955 0.684 ENR+CV-3 Ldha Cct8 0.644 0.264337282 0.288 0.674 0.311 ENR+CV-3 Cct8 Cd2ap 0.644 0.262480761 0.288 0.643 0.281 ENR+CV-3 Cd2ap Cox7a21 0.644 0.255700195 0.288 0.964 0.692 ENR+CV-3 Cox7a2 Prmt5 0.643 0.407067306 0.286 0.434 0.126 ENR+CV-3 Prmt5 Rabl6 0.643 0.348100347 0.286 0.475 0.157 ENR+CV-3 Rabl6 Atad3a 0.643 0.325756693 0.286 0.471 0.15 ENR+CV-3 Atad3a Fyttd1 0.643 0.304003921 0.286 0.489 0.166 ENR+CV-3 Fyttd1 Phb2 0.643 0.29687848 0.286 0.643 0.287 ENR+CV-3 Phb2 Ppm1g 0.643 0.28710945 0.286 0.48 0.154 ENR+CV-3 Ppm1g Ndufb10 0.643 0.283373315 0.286 0.584 0.235 ENR+CV-3 Ndufb10 Bola1 0.643 0.265556971 0.286 0.529 0.193 ENR+CV-3 Bola1 Hadha 0.643 0.253343852 0.286 0.611 0.259 ENR+CV-3 Hadha Agmat 0.642 0.533478721 0.284 0.353 0.062 ENR+CV-3 Agmat Gm10263 0.642 0.407675419 0.284 0.394 0.094 ENR+CV-3 Gm10263 Sephs2 0.642 0.382786254 0.284 0.448 0.138 ENR+CV-3 Sephs2 Tbcb 0.642 0.333854537 0.284 0.471 0.154 ENR+CV-3 Tbcb 2410006H16Rik 0.642 0.328988722 0.284 0.891 0.6 ENR+CV-3 2410006H16Rik Pdia4 0.642 0.328531061 0.284 0.575 0.242 ENR+CV-3 Pdia4 Cotl1 0.642 0.304644693 0.284 0.588 0.243 ENR+CV-3 Cotl1 Nucb1 0.642 0.295736178 0.284 0.498 0.172 ENR+CV-3 Nucb1 Gpa33 0.642 0.294875661 0.284 0.502 0.177 ENR+CV-3 Gpa33 Psmc5 0.642 0.292447264 0.284 0.552 0.214 ENR+CV-3 Psmc5 Rnf32 0.642 0.290946411 0.284 0.511 0.185 ENR+CV-3 Rnf32 Swi5 0.642 0.287036783 0.284 0.76 0.392 ENR+CV-3 Swi5 Khdrbs1 0.642 0.283789529 0.284 0.516 0.186 ENR+CV-3 Khdrbs1 Cd81 0.642 0.277677375 0.284 0.851 0.481 ENR+CV-3 Cd81 1810022K09Rik 0.642 0.273662337 0.284 0.756 0.383 ENR+CV-3 1810022K09Rik Ptp4a2 0.642 0.272261866 0.284 0.701 0.34 ENR+CV-3 Ptp4a2 Cct5 0.642 0.253198522 0.284 0.851 0.456 ENR+CV-3 Cct5 Pfdn2 0.641 0.399190242 0.282 0.434 0.129 ENR+CV-3 Pfdn2 Slc6a6 0.641 0.389936797 0.282 0.43 0.125 ENR+CV-3 Slc6a6 Aamp 0.641 0.316157004 0.282 0.489 0.172 ENR+CV-3 Aamp Gpi11 0.641 0.30168727 0.282 0.742 0.382 ENR+CV-3 Gpi1 Rps18-ps3 0.641 0.29936363 0.282 0.498 0.173 ENR+CV-3 Rps18-ps3 Rpl36-ps3 0.641 0.286796945 0.282 0.52 0.194 ENR+CV-3 Rpl36-ps3 Yme1l1 0.641 0.276923568 0.282 0.516 0.188 ENR+CV-3 Yme1l1 Arf5 0.641 0.275587472 0.282 0.611 0.262 ENR+CV-3 Arf5 Mrpl50 0.641 0.274480326 0.282 0.484 0.162 ENR+CV-3 Mrpl50 Sgta 0.64 0.376095148 0.28 0.43 0.127 ENR+CV-3 Sgta Dera 0.64 0.346430842 0.28 0.452 0.145 ENR+CV-3 Dera Bri3bp 0.64 0.308914611 0.28 0.439 0.128 ENR+CV-3 Bri3bp Paics 0.64 0.291080125 0.28 0.566 0.23 ENR+CV-3 Paics Ddit4 0.64 0.271961657 0.28 0.584 0.239 ENR+CV-3 Ddit4 Txnrd1 0.64 0.264857672 0.28 0.615 0.264 ENR+CV-3 Txnrd1 Hspa4 0.64 0.260914695 0.28 0.71 0.344 ENR+CV-3 Hspa4 Ywhae 0.64 0.254152661 0.28 0.873 0.472 ENR+CV-3 Ywhae Bdh1 0.639 0.408849677 0.278 0.416 0.119 ENR+CV-3 Bdh1 Alg5 0.639 0.405440815 0.278 0.425 0.127 ENR+CV-3 Alg5 Timm44 0.639 0.394476702 0.278 0.443 0.143 ENR+CV-3 Timm44 Foxa3 0.639 0.358262364 0.278 0.412 0.111 ENR+CV-3 Foxa3 Pik3r1 0.639 0.351660959 0.278 0.466 0.157 ENR+CV-3 Pik3r1 Dnttip2 0.639 0.348354516 0.278 0.502 0.187 ENR+CV-3 Dnttip2 Acsl3 0.639 0.34709397 0.278 0.425 0.122 ENR+CV-3 Acsl3 Rab7 0.639 0.343699796 0.278 0.466 0.158 ENR+CV-3 Rab7 Rpf2 0.639 0.335391152 0.278 0.457 0.151 ENR+CV-3 Rpf2 Pdcd5 0.639 0.312924478 0.278 0.493 0.175 ENR+CV-3 Pdcd5 Ddx39 0.639 0.302882185 0.278 0.484 0.169 ENR+CV-3 Ddx39 Rbm47 0.639 0.277911557 0.278 0.561 0.227 ENR+CV-3 Rbm47 Ndufs3 0.639 0.275305977 0.278 0.489 0.169 ENR+CV-3 Ndufs3 Commd6 0.639 0.266876047 0.278 0.516 0.191 ENR+CV-3 Commd6 Npc2 0.639 0.260223325 0.278 0.774 0.399 ENR+CV-3 Npc2 Hsp90b1 0.639 0.250429186 0.278 0.968 0.704 ENR+CV-3 Hsp90b1 Rnd3 0.638 0.409572262 0.276 0.407 0.112 ENR+CV-3 Rnd3 Fam32a 0.638 0.368268944 0.276 0.466 0.16 ENR+CV-3 Fam32a Slc31a1 0.638 0.354502771 0.276 0.416 0.117 ENR+CV-3 Slc31a1 Ankrd10 0.638 0.344810576 0.276 0.371 0.08 ENR+CV-3 Ankrd10 Eci2 0.638 0.335670906 0.276 0.425 0.124 ENR+CV-3 Eci2 Galnt7 0.638 0.329784345 0.276 0.448 0.143 ENR+CV-3 Galnt7 Rab5c 0.638 0.328865173 0.276 0.425 0.124 ENR+CV-3 Rab5c Ssrp1 0.638 0.286622219 0.276 0.588 0.25 ENR+CV-3 Ssrp1 Phgdh 0.638 0.272401728 0.276 0.48 0.162 ENR+CV-3 Phgdh Etfa 0.638 0.265488845 0.276 0.597 0.259 ENR+CV-3 Etfa Prdx2 0.638 0.257569695 0.276 0.882 0.531 ENR+CV-3 Prdx2 Tomm5 0.638 0.255195027 0.276 0.629 0.279 ENR+CV-3 Tomm5 Gm2a 0.637 0.442542039 0.274 0.33 0.049 ENR+CV-3 Gm2a Atf31 0.637 0.437550899 0.274 0.561 0.253 ENR+CV-3 Atf3 Smn1 0.637 0.426463376 0.274 0.389 0.102 ENR+CV-3 Smn1 Fam13a 0.637 0.404221351 0.274 0.367 0.079 ENR+CV-3 Fam13a Wdr45b 0.637 0.387586209 0.274 0.385 0.095 ENR+CV-3 Wdr45b Dhrs7 0.637 0.364690226 0.274 0.403 0.108 ENR+CV-3 Dhrs7 Glg1 0.637 0.33486882 0.274 0.43 0.13 ENR+CV-3 Glg1 Eif2a 0.637 0.309781091 0.274 0.48 0.171 ENR+CV-3 Eif2a Sepw1 0.637 0.280746054 0.274 0.652 0.303 ENR+CV-3 Sepw1 Fbp2 0.637 0.25504568 0.274 0.529 0.207 ENR+CV-3 Fbp2 Cdh17 0.637 0.253382194 0.274 0.575 0.236 ENR+CV-3 Cdh17 Nmt1 0.636 0.359317216 0.272 0.443 0.146 ENR+CV-3 Nmt1 Scd21 0.636 0.345455069 0.272 0.869 0.525 ENR+CV-3 Scd2 Rae1 0.636 0.329458425 0.272 0.403 0.109 ENR+CV-3 Rae1 Sfr1 0.636 0.316313039 0.272 0.507 0.193 ENR+CV-3 Sfr1 Mcm7 0.636 0.306503784 0.272 0.452 0.148 ENR+CV-3 Mcm7 Mapre1 0.636 0.276078958 0.272 0.507 0.187 ENR+CV-3 Mapre1 Sox9 0.636 0.275217565 0.272 0.606 0.267 ENR+CV-3 Sox9 Tpd52 0.636 0.271598637 0.272 0.774 0.42 ENR+CV-3 Tpd52 Adipor1 0.636 0.265255848 0.272 0.525 0.203 ENR+CV-3 Adipor1 Aplp2 0.636 0.265198365 0.272 0.606 0.27 ENR+CV-3 Aplp2 Marcksl1 0.636 0.263325643 0.272 0.502 0.181 ENR+CV-3 Marcksl1 Psmd14 0.636 0.251104443 0.272 0.561 0.231 ENR+CV-3 Psmd14 Mpnd1 0.635 0.460902238 0.27 0.38 0.096 ENR+CV-3 Mpnd Prkar2a 0.635 0.365478848 0.27 0.407 0.118 ENR+CV-3 Prkar2a Pgrmc2 0.635 0.363070874 0.27 0.434 0.138 ENR+CV-3 Pgrmc2 Ilf2 0.635 0.344787264 0.27 0.466 0.165 ENR+CV-3 Ilf2 Brix1 0.635 0.329196212 0.27 0.434 0.138 ENR+CV-3 Brix1 Utp11l 0.635 0.327863946 0.27 0.443 0.146 ENR+CV-3 Utp11l Arl1 0.635 0.293064664 0.27 0.466 0.161 ENR+CV-3 Arl1 Gars 0.635 0.28182193 0.27 0.579 0.252 ENR+CV-3 Gars Arpc5l 0.635 0.251685865 0.27 0.507 0.19 ENR+CV-3 Arpc5l Mpzl1 0.634 0.393191521 0.268 0.398 0.115 ENR+CV-3 Mpzl1 Sqle 0.634 0.29708436 0.268 0.471 0.166 ENR+CV-3 Sqle Anp32e 0.634 0.277062793 0.268 0.511 0.197 ENR+CV-3 Anp32e Actn1 0.634 0.266530162 0.268 0.484 0.174 ENR+CV-3 Actn1 Dkc1 0.634 0.262720409 0.268 0.502 0.189 ENR+CV-3 Dkc1 B4galnt2 0.633 0.349955278 0.266 0.403 0.115 ENR+CV-3 B4galnt2 Psmd2 0.633 0.343364013 0.266 0.462 0.165 ENR+CV-3 Psmd2 Hes6 0.633 0.336088371 0.266 0.507 0.208 ENR+CV-3 Hes6 Pes1 0.633 0.333617268 0.266 0.421 0.13 ENR+CV-3 Pes1 Fam104a 0.633 0.313868511 0.266 0.439 0.144 ENR+CV-3 Fam104a Pfkl 0.633 0.310615413 0.266 0.475 0.174 ENR+CV-3 Pfkl Hspa5 0.633 0.295436816 0.266 0.928 0.666 ENR+CV-3 Hspa5 Atp6v1a 0.633 0.293983742 0.266 0.407 0.118 ENR+CV-3 Atp6v1a Aig1 0.633 0.288333287 0.266 0.434 0.139 ENR+CV-3 Aig1 Ddx24 0.633 0.280144629 0.266 0.457 0.156 ENR+CV-3 Ddx24 Hnrnpf 0.633 0.272028352 0.266 0.548 0.226 ENR+CV-3 Hnrnpf Sarnp 0.633 0.271213172 0.266 0.475 0.169 ENR+CV-3 Sarnp Vcp 0.633 0.258540848 0.266 0.575 0.249 ENR+CV-3 Vcp 2700060E02Rik 0.633 0.256336656 0.266 0.765 0.415 ENR+CV-3 2700060E02Rik Sod2 0.633 0.252480444 0.266 0.493 0.185 ENR+CV-3 Sod2 Amn 0.632 0.422108076 0.264 0.339 0.065 ENR+CV-3 Amn Clic6 0.632 0.413717007 0.264 0.371 0.096 ENR+CV-3 Clic6 Nob1 0.632 0.350049824 0.264 0.376 0.094 ENR+CV-3 Nob1 Nudc 0.632 0.289837676 0.264 0.475 0.172 ENR+CV-3 Nudc Nars 0.632 0.275312013 0.264 0.814 0.477 ENR+CV-3 Nars Psmd1 0.632 0.27330622 0.264 0.493 0.188 ENR+CV-3 Psmd1 Me2 0.632 0.273097535 0.264 0.448 0.153 ENR+CV-3 Me2 Ndufa9 0.632 0.272242558 0.264 0.452 0.155 ENR+CV-3 Ndufa9 Rab1 0.632 0.268337852 0.264 0.579 0.255 ENR+CV-3 Rab1 Lgr5 0.632 0.253999276 0.264 0.475 0.171 ENR+CV-3 Lgr5 B3galtl 0.631 0.421534581 0.262 0.33 0.06 ENR+CV-3 B3galtl Ralgps2 0.631 0.382368518 0.262 0.371 0.093 ENR+CV-3 Ralgps2 Fads1 0.631 0.368838744 0.262 0.394 0.115 ENR+CV-3 Fads1 Rbm34 0.631 0.357864852 0.262 0.416 0.133 ENR+CV-3 Rbm34 Acp1 0.631 0.325332684 0.262 0.457 0.165 ENR+CV-3 Acp1 Trnt1 0.631 0.31780767 0.262 0.412 0.128 ENR+CV-3 Trnt1 Mrps18a 0.631 0.306025225 0.262 0.421 0.132 ENR+CV-3 Mrps18a Kcnq11 0.631 0.305219535 0.262 0.448 0.156 ENR+CV-3 Kcnq1 Prkcsh 0.631 0.304924765 0.262 0.466 0.17 ENR+CV-3 Prkcsh Zfp106 0.631 0.297963124 0.262 0.475 0.178 ENR+CV-3 Zfp106 Tsn 0.631 0.293628677 0.262 0.48 0.184 ENR+CV-3 Tsn Pkn2 0.631 0.26132162 0.262 0.448 0.153 ENR+CV-3 Pkn2 Psma3 0.631 0.252628847 0.262 0.471 0.169 ENR+CV-3 Psma3 Ociad2 0.631 0.252431317 0.262 0.471 0.17 ENR+CV-3 Ociad2 Vapb 0.63 0.330218733 0.26 0.398 0.117 ENR+CV-3 Vapb Mrps33 0.63 0.322138126 0.26 0.407 0.124 ENR+CV-3 Mrps33 Nfia 0.629 0.372344905 0.258 0.403 0.126 ENR+CV-3 Nfia Dpysl2 0.629 0.357662173 0.258 0.394 0.116 ENR+CV-3 Dpysl2 Nsdhl 0.629 0.335956565 0.258 0.367 0.093 ENR+CV-3 Nsdhl Ccdc59 0.629 0.317569242 0.258 0.416 0.134 ENR+CV-3 Ccdc59 Prpf19 0.629 0.28960532 0.258 0.48 0.186 ENR+CV-3 Prpf19 Ppil1 0.629 0.279161865 0.258 0.416 0.13 ENR+CV-3 Ppil1 Slc12a2 0.629 0.267494012 0.258 0.837 0.496 ENR+CV-3 Slc12a2 Zfp91 0.629 0.266726186 0.258 0.502 0.203 ENR+CV-3 Zfp91 Atp5l 0.629 0.265186965 0.258 0.538 0.228 ENR+CV-3 Atp5l Polr1c 0.628 0.32267448 0.256 0.38 0.104 ENR+CV-3 Polr1c Szrd1 0.628 0.314005056 0.256 0.398 0.119 ENR+CV-3 Szrd1 Tmod3 0.628 0.262672408 0.256 0.457 0.165 ENR+CV-3 Tmod3 Eif3l 0.628 0.254619945 0.256 0.579 0.261 ENR+CV-3 Eif3l Rps4y2 0.627 0.369445785 0.254 0.389 0.116 ENR+CV-3 Rps4y2 Brd7 0.627 0.336291517 0.254 0.394 0.118 ENR+CV-3 Brd7 RP24-176F12.14 0.627 0.318702184 0.254 0.376 0.104 ENR+CV-3 RP24-176F12.14 Tra2b 0.627 0.308633265 0.254 0.538 0.241 ENR+CV-3 Tra2b Polr2i 0.627 0.305887341 0.254 0.43 0.148 ENR+CV-3 Polr2i Pnkd 0.627 0.289044897 0.254 0.398 0.12 ENR+CV-3 Pnkd Gm11808 0.627 0.280317569 0.254 0.484 0.191 ENR+CV-3 Gm11808 Magohb 0.627 0.274427447 0.254 0.385 0.109 ENR+CV-3 Magohb Npepps 0.627 0.272387869 0.254 0.448 0.16 ENR+CV-3 Npepps Sae1 0.627 0.256222215 0.254 0.516 0.21 ENR+CV-3 Sae1 Desi2 0.626 0.414731718 0.252 0.339 0.077 ENR+CV-3 Desi2 Mpst 0.626 0.364949377 0.252 0.321 0.059 ENR+CV-3 Mpst Cetn2 0.626 0.339756681 0.252 0.394 0.122 ENR+CV-3 Cetn2 Elp5 0.626 0.333591369 0.252 0.362 0.093 ENR+CV-3 Elp5 Gar1 0.626 0.328173435 0.252 0.376 0.106 ENR+CV-3 Gar1 Alkbh5 0.626 0.319023862 0.252 0.416 0.139 ENR+CV-3 Alkbh5 Snx2 0.626 0.26982392 0.252 0.398 0.122 ENR+CV-3 Snx2 Plod2 0.625 0.491981948 0.25 0.29 0.036 ENR+CV-3 Plod2 Gm22426 0.625 0.433954831 0.25 0.299 0.044 ENR+CV-3 Gm22426 Pld3 0.625 0.359197611 0.25 0.357 0.092 ENR+CV-3 Pld3 Yrdc 0.625 0.358995577 0.25 0.357 0.093 ENR+CV-3 Yrdc Sbno1 0.625 0.290746042 0.25 0.475 0.187 ENR+CV-3 Sbno1 Plin3 0.625 0.28080554 0.25 0.416 0.138 ENR+CV-3 Plin3 Pdgfa 0.625 0.278929754 0.25 0.597 0.289 ENR+CV-3 Pdgfa Galm 0.624 0.319336332 0.248 0.371 0.105 ENR+CV-3 Galm Gcat1 0.624 0.292233697 0.248 0.452 0.172 ENR+CV-3 Gcat Por1 0.624 0.286876979 0.248 0.443 0.164 ENR+CV-3 Por Timm10b 0.624 0.272168866 0.248 0.443 0.162 ENR+CV-3 Timm10b Stk38 0.623 0.37447416 0.246 0.348 0.089 ENR+CV-3 Stk38 Tnpo3 0.623 0.360966642 0.246 0.362 0.1 ENR+CV-3 Tnpo3 Pphln1 0.623 0.351582995 0.246 0.326 0.069 ENR+CV-3 Pphln1 Scd11 0.623 0.346466 0.246 0.367 0.102 ENR+CV-3 Scd1 Tcof1 0.623 0.306197939 0.246 0.398 0.128 ENR+CV-3 Tcof1 Ncln 0.623 0.300110241 0.246 0.38 0.115 ENR+CV-3 Ncln Lrig1 0.623 0.296665618 0.246 0.412 0.138 ENR+CV-3 Lrig1 Uck2 0.623 0.294847078 0.246 0.407 0.137 ENR+CV-3 Uck2 Fxr1 0.623 0.283047586 0.246 0.416 0.142 ENR+CV-3 Fxr1 Qdpr 0.623 0.26875615 0.246 0.439 0.162 ENR+CV-3 Qdpr Tmprss4 0.623 0.254359478 0.246 0.412 0.136 ENR+CV-3 Tmprss4 Zfand6 0.623 0.25170891 0.246 0.462 0.179 ENR+CV-3 Zfand6 Tmem261 0.623 0.251224785 0.246 0.443 0.164 ENR+CV-3 Tmem261 Prox1 0.622 0.416870183 0.244 0.38 0.117 ENR+CV-3 Prox1 Seh1l 0.622 0.340132025 0.244 0.357 0.098 ENR+CV-3 Seh1l Klhdc2 0.622 0.30307816 0.244 0.394 0.126 ENR+CV-3 Klhdc2 Ndufaf4 0.622 0.288337133 0.244 0.394 0.126 ENR+CV-3 Ndufaf4 Cryzl1 0.622 0.28002871 0.244 0.371 0.106 ENR+CV-3 Cryzl1 Ndfip2 0.622 0.278660582 0.244 0.385 0.119 ENR+CV-3 Ndfip2 Raly 0.622 0.26685766 0.244 0.434 0.159 ENR+CV-3 Raly Prlr 0.621 0.397356898 0.242 0.326 0.074 ENR+CV-3 Prlr Kdm5b 0.621 0.361426418 0.242 0.367 0.108 ENR+CV-3 Kdm5b Asna1 0.621 0.335721761 0.242 0.362 0.104 ENR+CV-3 Asna1 Zfp703 0.621 0.318732988 0.242 0.367 0.107 ENR+CV-3 Zfp703 Dap 0.621 0.312117704 0.242 0.348 0.091 ENR+CV-3 Dap Lrrc59 0.621 0.3107705 0.242 0.376 0.112 ENR+CV-3 Lrrc59 Hibadh 0.621 0.308437617 0.242 0.398 0.135 ENR+CV-3 Hibadh Pdcd4 0.621 0.306418693 0.242 0.443 0.172 ENR+CV-3 Pdcd4 Efr3a 0.621 0.297326411 0.242 0.367 0.105 ENR+CV-3 Efr3a Emc2 0.621 0.272014463 0.242 0.376 0.114 ENR+CV-3 Emc2 Snx1 0.621 0.26623895 0.242 0.394 0.128 ENR+CV-3 Snx1 Atp6ap2 0.621 0.265413821 0.242 0.462 0.181 ENR+CV-3 Atp6ap2 Rnf6 0.621 0.251243163 0.242 0.376 0.113 ENR+CV-3 Rnf6 Ntmt1 0.62 0.408945897 0.24 0.326 0.077 ENR+CV-3 Ntmt1 Lhpp 0.62 0.399587024 0.24 0.312 0.065 ENR+CV-3 Lhpp Rassf4 0.62 0.364120801 0.24 0.312 0.063 ENR+CV-3 Rassf4 Elovl1 0.62 0.337464335 0.24 0.362 0.105 ENR+CV-3 Elovl1 Wbp11 0.62 0.277567753 0.24 0.412 0.143 ENR+CV-3 Wbp11 Mrpl22 0.62 0.251906734 0.24 0.362 0.102 ENR+CV-3 Mrpl22 Ikbkap 0.619 0.411348721 0.238 0.303 0.059 ENR+CV-3 Ikbkap Naf1 0.619 0.390331237 0.238 0.303 0.056 ENR+CV-3 Naf1 Rrp15 0.619 0.35492878 0.238 0.321 0.072 ENR+CV-3 Rrp15 Cdk6 0.619 0.345788648 0.238 0.344 0.093 ENR+CV-3 Cdk6 Rfc3 0.619 0.342265028 0.238 0.389 0.131 ENR+CV-3 Rfc3 Ufsp2 0.619 0.32017561 0.238 0.367 0.11 ENR+CV-3 Ufsp2 Stx7 0.619 0.312131727 0.238 0.394 0.134 ENR+CV-3 Stx7 Nop16 0.619 0.294292884 0.238 0.389 0.129 ENR+CV-3 Nop16 Slc5a1 0.619 0.270388417 0.238 0.421 0.154 ENR+CV-3 Slc5a1 Aup1 0.619 0.268483214 0.238 0.439 0.168 ENR+CV-3 Aup1 Fkbp8 0.619 0.257443894 0.238 0.466 0.191 ENR+CV-3 Fkbp8 Cdk2ap2 0.619 0.256512074 0.238 0.425 0.155 ENR+CV-3 Cdk2ap2 Klf3 0.618 0.351367814 0.236 0.335 0.087 ENR+CV-3 Klf3 0610031J06Rik 0.618 0.346276069 0.236 0.344 0.094 ENR+CV-3 0610031J06Rik Hmga1 0.618 0.339561037 0.236 0.344 0.095 ENR+CV-3 Hmga1 Exosc4 0.618 0.333259277 0.236 0.335 0.084 ENR+CV-3 Exosc4 Hexim1 0.618 0.331104877 0.236 0.371 0.117 ENR+CV-3 Hexim1 Tmem66 0.618 0.320639412 0.236 0.376 0.121 ENR+CV-3 Tmem66 Leprot 0.618 0.320018935 0.236 0.344 0.094 ENR+CV-3 Leprot Mrpl2 0.618 0.293530504 0.236 0.362 0.108 ENR+CV-3 Mrpl2 Thop1 0.618 0.291395301 0.236 0.339 0.087 ENR+CV-3 Thop1 Acat2 0.618 0.282959794 0.236 0.376 0.118 ENR+CV-3 Acat2 Spop 0.618 0.27614651 0.236 0.416 0.154 ENR+CV-3 Spop Elf1 0.618 0.270267669 0.236 0.394 0.133 ENR+CV-3 Elf1 Net1 0.618 0.26541165 0.236 0.425 0.161 ENR+CV-3 Net1 Gsr 0.618 0.259679394 0.236 0.457 0.185 ENR+CV-3 Gsr U2af2 0.618 0.255860477 0.236 0.385 0.124 ENR+CV-3 U2af2 Msx1 0.617 0.468030677 0.234 0.285 0.045 ENR+CV-3 Msx1 Grn 0.617 0.340436379 0.234 0.335 0.087 ENR+CV-3 Grn 4833439L19Rik 0.617 0.337882454 0.234 0.357 0.109 ENR+CV-3 4833439L19Rik Fam136a 0.617 0.310596901 0.234 0.421 0.16 ENR+CV-3 Fam136a Btg1 0.617 0.300644016 0.234 0.416 0.156 ENR+CV-3 Btg1 Timm50 0.617 0.294942893 0.234 0.394 0.137 ENR+CV-3 Timm50 Dlat 0.617 0.272947513 0.234 0.376 0.121 ENR+CV-3 Dlat Higd1a 0.617 0.255700338 0.234 0.407 0.144 ENR+CV-3 Higd1a D10Wsu102e 0.616 0.372360998 0.232 0.317 0.075 ENR+CV-3 D10Wsu102e Tst 0.616 0.334046744 0.232 0.299 0.058 ENR+CV-3 Tst Elovl5 0.616 0.326040888 0.232 0.33 0.085 ENR+CV-3 Elovl5 Fam96b 0.616 0.311746555 0.232 0.362 0.114 ENR+CV-3 Fam96b Suclg2 0.616 0.285130677 0.232 0.376 0.122 ENR+CV-3 Suclg2 Sigmar1 0.616 0.269596127 0.232 0.344 0.094 ENR+CV-3 Sigmar1 Ppie 0.616 0.269023298 0.232 0.367 0.114 ENR+CV-3 Ppie Asnsd1 0.616 0.260858767 0.232 0.376 0.122 ENR+CV-3 Asnsd1 Igf2r 0.616 0.25663532 0.232 0.389 0.134 ENR+CV-3 Igf2r Mex3a 0.615 0.433430778 0.23 0.29 0.053 ENR+CV-3 Mex3a Ccz1 0.615 0.350533738 0.23 0.344 0.101 ENR+CV-3 Ccz1 Rapgef6 0.615 0.33230009 0.23 0.344 0.099 ENR+CV-3 Rapgef6 Dnajc22 0.615 0.296784797 0.23 0.385 0.134 ENR+CV-3 Dnajc22 Gna11 0.615 0.258355419 0.23 0.376 0.121 ENR+CV-3 Gna11 1110001A16Rik 0.615 0.25286696 0.23 0.394 0.139 ENR+CV-3 1110001A16Rik Tmem171 0.614 0.352367097 0.228 0.299 0.061 ENR+CV-3 Tmem171 Id2 0.614 0.334716711 0.228 0.416 0.162 ENR+CV-3 Id2 Pmvk 0.614 0.329991942 0.228 0.344 0.102 ENR+CV-3 Pmvk Blmh 0.614 0.270990381 0.228 0.371 0.121 ENR+CV-3 Blmh Slc38a1 0.614 0.254568558 0.228 0.43 0.17 ENR+CV-3 Slc38a1 Acads 0.613 0.324186672 0.226 0.33 0.092 ENR+CV-3 Acads Lsm7 0.613 0.302123591 0.226 0.335 0.096 ENR+CV-3 Lsm7 Snx4 0.613 0.294212817 0.226 0.376 0.131 ENR+CV-3 Snx4 Dnpep 0.613 0.276265733 0.226 0.348 0.105 ENR+CV-3 Dnpep Homer2 0.613 0.27548174 0.226 0.403 0.151 ENR+CV-3 Homer2 Sssca1 0.613 0.266419115 0.226 0.353 0.109 ENR+CV-3 Sssca1 Srm 0.612 0.320701033 0.224 0.362 0.118 ENR+CV-3 Srm Eif2b4 0.612 0.319058884 0.224 0.33 0.092 ENR+CV-3 Eif2b4 Pold2 0.612 0.310170337 0.224 0.339 0.099 ENR+CV-3 Pold2 Ltv1 0.612 0.2869893 0.224 0.335 0.096 ENR+CV-3 Ltv1 Abi1 0.612 0.282020168 0.224 0.376 0.13 ENR+CV-3 Abi1 Id3 0.612 0.278098076 0.224 0.489 0.22 ENR+CV-3 Id3 Trib1 0.612 0.272703162 0.224 0.357 0.113 ENR+CV-3 Trib1 Pgd 0.612 0.263513383 0.224 0.439 0.183 ENR+CV-3 Pgd Aimp2 0.612 0.250744234 0.224 0.394 0.145 ENR+CV-3 Aimp2 Scpep1 0.611 0.321104092 0.222 0.321 0.087 ENR+CV-3 Scpep1 Pcbd2 0.611 0.31640147 0.222 0.335 0.098 ENR+CV-3 Pcbd2 Itpr31 0.611 0.285304682 0.222 0.353 0.111 ENR+CV-3 Itpr3 Rfc2 0.611 0.266888028 0.222 0.367 0.124 ENR+CV-3 Rfc2 Man1a 0.611 0.262321764 0.222 0.344 0.105 ENR+CV-3 Man1a Epb4.1l3 0.611 0.259302568 0.222 0.389 0.143 ENR+CV-3 Epb4.1l3 mt-Tq1 0.61 0.40426559 0.22 0.267 0.042 ENR+CV-3 mt-Tq Rbm38 0.61 0.362559847 0.22 0.299 0.07 ENR+CV-3 Rbm38 Zfp36l2 0.61 0.341893789 0.22 0.367 0.127 ENR+CV-3 Zfp36l2 Stk38l 0.61 0.322543455 0.22 0.303 0.072 ENR+CV-3 Stk38l Nufip2 0.61 0.322270517 0.22 0.348 0.113 ENR+CV-3 Nufip2 Wwp1 0.61 0.292019818 0.22 0.353 0.117 ENR+CV-3 Wwp1 Gtl3 0.61 0.273809159 0.22 0.371 0.129 ENR+CV-3 Gtl3 Psmd13 0.61 0.268493546 0.22 0.385 0.141 ENR+CV-3 Psmd13 Abcd3 0.61 0.250521568 0.22 0.394 0.147 ENR+CV-3 Abcd3 Tubb2b 0.609 0.404769251 0.218 0.285 0.061 ENR+CV-3 Tubb2b Mfsd1 0.609 0.325334218 0.218 0.312 0.082 ENR+CV-3 Mfsd1 Mtfp1 0.609 0.324482132 0.218 0.281 0.056 ENR+CV-3 Mtfp1 Saysd1 0.609 0.306817574 0.218 0.308 0.078 ENR+CV-3 Saysd1 Vat1 0.609 0.280575618 0.218 0.294 0.064 ENR+CV-3 Vat1 Med10 0.609 0.277896986 0.218 0.33 0.097 ENR+CV-3 Med10 Snrpc 0.609 0.266562146 0.218 0.362 0.123 ENR+CV-3 Snrpc Acadvl 0.609 0.26563737 0.218 0.33 0.096 ENR+CV-3 Acadvl Wdr12 0.608 0.292666818 0.216 0.344 0.113 ENR+CV-3 Wdr12 Senp2 0.608 0.289581275 0.216 0.33 0.1 ENR+CV-3 Senp2 Pum1 0.608 0.287760438 0.216 0.357 0.122 ENR+CV-3 Pum1 Pigt 0.608 0.286777318 0.216 0.317 0.089 ENR+CV-3 Pigt Camta1 0.607 0.323001702 0.214 0.281 0.059 ENR+CV-3 Camta1 Mvd 0.607 0.312656662 0.214 0.299 0.073 ENR+CV-3 Mvd Irf8 0.607 0.309223965 0.214 0.303 0.079 ENR+CV-3 Irf8 Mpzl2 0.607 0.283260694 0.214 0.335 0.105 ENR+CV-3 Mpzl2 Tmem242 0.607 0.261007344 0.214 0.353 0.121 ENR+CV-3 Tmem242 Cpox 0.606 0.317825012 0.212 0.326 0.1 ENR+CV-3 Cpox Tmem57 0.606 0.290728898 0.212 0.308 0.084 ENR+CV-3 Tmem57 Snrpa 0.605 0.327393024 0.21 0.33 0.108 ENR+CV-3 Snrpa Tns3 0.605 0.277191665 0.21 0.33 0.104 ENR+CV-3 Tns3 Smek2 0.605 0.254570889 0.21 0.398 0.164 ENR+CV-3 Smek2 Csnk2a2 0.604 0.407357302 0.208 0.262 0.049 ENR+CV-3 Csnk2a2 Lgals1 0.604 0.394722012 0.208 0.267 0.053 ENR+CV-3 Lgals1 Arl4a 0.604 0.328339808 0.208 0.317 0.096 ENR+CV-3 Arl4a Cited2 0.604 0.303362787 0.208 0.294 0.074 ENR+CV-3 Cited2 Tceal8 0.604 0.298448901 0.208 0.33 0.108 ENR+CV-3 Tceal8 Casp3 0.604 0.280017387 0.208 0.308 0.087 ENR+CV-3 Casp3 Cisd1 0.604 0.275596402 0.208 0.357 0.129 ENR+CV-3 Cisd1 Cyb561 0.604 0.261953768 0.208 0.29 0.071 ENR+CV-3 Cyb561 Dag1 0.604 0.252119133 0.208 0.339 0.114 ENR+CV-3 Dag1 Gramd3 0.603 0.333171151 0.206 0.281 0.067 ENR+CV-3 Gramd3 Trim37 0.603 0.301015518 0.206 0.308 0.089 ENR+CV-3 Trim37 Usp33 0.603 0.271767928 0.206 0.326 0.105 ENR+CV-3 Usp33 Psenen 0.603 0.269489223 0.206 0.29 0.073 ENR+CV-3 Psenen Rbbp8 0.603 0.255932171 0.206 0.308 0.088 ENR+CV-3 Rbbp8 Crlf1 0.602 0.425309976 0.204 0.24 0.034 ENR+CV-3 Crlf1 Cd82 0.602 0.288228889 0.204 0.308 0.091 ENR+CV-3 Cd82 Znrf2 0.602 0.260124534 0.204 0.312 0.094 ENR+CV-3 Znrf2 Shmt1 0.602 0.251927386 0.204 0.344 0.121 ENR+CV-3 Shmt1 Abhd17a 0.601 0.259082574 0.202 0.33 0.111 ENR+CV-3 Abhd17a Pdk1 0.601 0.253925716 0.202 0.348 0.127 ENR+CV-3 Pdk1 Nubp1 0.601 0.250201216 0.202 0.33 0.113 ENR+CV-3 Nubp1 Rpl413 0.914 1.27710129 0.828 0.991 0.822 ENR+CV-4 Rpl41 Pabpc13 0.91 0.987057951 0.82 1 0.797 ENR+CV-4 Pabpc1 Tubb52 0.879 1.079830906 0.758 0.991 0.584 ENR+CV-4 Tubb5 Gm20003 0.873 1.138545443 0.746 0.963 0.437 ENR+CV-4 Gm2000 Gm269243 0.873 0.917007836 0.746 1 0.935 ENR+CV-4 Gm26924 Rpl37a3 0.864 0.923564177 0.728 0.986 0.584 ENR+CV-4 Rpl37a Top2a 0.833 1.063774035 0.666 0.936 0.311 ENR+CV-4 Top2a H1f03 0.82 1.014029909 0.64 0.922 0.37 ENR+CV-4 H1f0 Smoc22 0.819 0.912134984 0.638 0.95 0.435 ENR+CV-4 Smoc2 Uqcr102 0.818 0.750489221 0.636 1 0.668 ENR+CV-4 Uqcr10 2810417H13Rik 0.817 1.118599214 0.634 0.839 0.23 ENR+CV-4 2810417H13Rik Dbi3 0.817 0.635827462 0.634 1 0.818 ENR+CV-4 Dbi Gm155643 0.816 0.862925758 0.632 0.867 0.202 ENR+CV-4 Gm15564 Smc4 0.814 0.939051587 0.628 0.908 0.26 ENR+CV-4 Smc4 Rpph12 0.808 0.46376516 0.616 0.963 0.379 ENR+CV-4 Rpph1 Bola23 0.793 0.789188442 0.586 0.899 0.289 ENR+CV-4 Bola2 Taldo12 0.791 0.7520657 0.582 0.945 0.427 ENR+CV-4 Taldo1 Uqcr112 0.791 0.67996669 0.582 0.968 0.626 ENR+CV-4 Uqcr11 Hmgb12 0.789 0.915811857 0.578 0.826 0.242 ENR+CV-4 Hmgb1 Gm100762 0.788 0.722580202 0.576 0.963 0.607 ENR+CV-4 Gm10076 Rpl35a2 0.788 0.629467239 0.576 0.977 0.783 ENR+CV-4 Rpl35a Mlec2 0.785 0.753675464 0.57 0.936 0.354 ENR+CV-4 Mlec Hes13 0.776 0.979220055 0.552 0.775 0.216 ENR+CV-4 Hes1 Bex12 0.771 0.75160367 0.542 0.853 0.273 ENR+CV-4 Bex1 Rpl372 0.769 0.623370319 0.538 0.959 0.651 ENR+CV-4 Rpl37 Mki67 0.767 0.788146731 0.534 0.853 0.296 ENR+CV-4 Mki67 Ifitm22 0.763 0.619884638 0.526 0.986 0.545 ENR+CV-4 Ifitm2 Psmc31 0.76 0.7190257 0.52 0.78 0.22 ENR+CV-4 Psmc3 Hist1h1b 0.759 0.885790981 0.518 0.693 0.151 ENR+CV-4 Hist1h1b Smc2 0.756 0.697876671 0.512 0.725 0.163 ENR+CV-4 Smc2 Dynll21 0.756 0.689622449 0.512 0.817 0.265 ENR+CV-4 Dynll2 Cox4i12 0.756 0.450685885 0.512 0.991 0.852 ENR+CV-4 Cox4i1 Egr13 0.754 0.762185697 0.508 0.876 0.391 ENR+CV-4 Egr1 Cox6a12 0.752 0.500037044 0.504 0.982 0.701 ENR+CV-4 Cox6a1 Psmc13 0.751 0.706706977 0.502 0.775 0.234 ENR+CV-4 Psmc1 Uqcrc12 0.751 0.603530854 0.502 0.931 0.413 ENR+CV-4 Uqcrc1 Wbp52 0.751 0.598776284 0.502 0.963 0.491 ENR+CV-4 Wbp5 Ptma3 0.749 0.52115301 0.498 0.963 0.735 ENR+CV-4 Ptma Nusap1 0.748 0.875835989 0.496 0.615 0.097 ENR+CV-4 Nusap1 Idh3a1 0.748 0.62531889 0.496 0.761 0.21 ENR+CV-4 Idh3a Sypl1 0.748 0.624209872 0.496 0.917 0.39 ENR+CV-4 Sypl Serinc32 0.747 0.666831341 0.494 0.927 0.48 ENR+CV-4 Serinc3 Ak22 0.747 0.649696188 0.494 0.812 0.278 ENR+CV-4 Ak2 Atp5k2 0.747 0.623960273 0.494 0.913 0.469 ENR+CV-4 Atp5k Uqcrq2 0.745 0.48641841 0.49 0.995 0.755 ENR+CV-4 Uqcrq Rpl132 0.745 0.413951895 0.49 0.991 0.905 ENR+CV-4 Rpl13 Idh21 0.744 0.660825146 0.488 0.766 0.228 ENR+CV-4 Idh2 Tmem971 0.744 0.614696525 0.488 0.78 0.237 ENR+CV-4 Tmem97 Ndufb42 0.743 0.694175013 0.486 0.789 0.262 ENR+CV-4 Ndufb4 Ndufb82 0.742 0.571997471 0.484 0.94 0.502 ENR+CV-4 Ndufb8 Atp5o2 0.742 0.532588249 0.484 0.954 0.526 ENR+CV-4 Atp5o Ybx13 0.741 0.563247665 0.482 0.954 0.727 ENR+CV-4 Ybx1 Rny13 0.741 0.562935888 0.482 0.587 0.082 ENR+CV-4 Rny1 Snord133 0.74 0.697563844 0.48 0.674 0.171 ENR+CV-4 Snord13 Tpi13 0.74 0.578456184 0.48 0.968 0.582 ENR+CV-4 Tpi1 Gm98462 0.739 0.743380999 0.478 0.619 0.115 ENR+CV-4 Gm9846 Prc1 0.739 0.719942861 0.478 0.628 0.116 ENR+CV-4 Prc1 Mdh22 0.739 0.589122035 0.478 0.904 0.395 ENR+CV-4 Mdh2 Hmgb2 0.736 0.6253128 0.472 0.922 0.479 ENR+CV-4 Hmgb2 Hmgcs23 0.735 0.806516034 0.47 0.592 0.101 ENR+CV-4 Hmgcs2 Ccdc342 0.734 0.616465377 0.468 0.885 0.42 ENR+CV-4 Ccdc34 Tmem2562 0.734 0.589648713 0.468 0.872 0.381 ENR+CV-4 Tmem256 Cbx11 0.734 0.563672515 0.468 0.826 0.298 ENR+CV-4 Cbx1 Pcsk92 0.733 0.60991063 0.466 0.665 0.158 ENR+CV-4 Pcsk9 Csnk2a11 0.732 0.649642724 0.464 0.656 0.153 ENR+CV-4 Csnk2a1 Tuba1c 0.731 0.647405482 0.462 0.876 0.387 ENR+CV-4 Tuba1c H2-Q102 0.73 0.665684835 0.46 0.606 0.117 ENR+CV-4 H2-Q10 H2afv1 0.73 0.580617561 0.46 0.872 0.385 ENR+CV-4 H2afv Arpp193 0.73 0.551691056 0.46 0.858 0.339 ENR+CV-4 Arpp19 Rpl342 0.729 0.436853753 0.458 0.968 0.815 ENR+CV-4 Rpl34 Gcat2 0.728 0.602060203 0.456 0.661 0.164 ENR+CV-4 Gcat Nucks1 0.728 0.539838631 0.456 0.83 0.307 ENR+CV-4 Nucks1 Cdca8 0.727 0.594264131 0.454 0.647 0.149 ENR+CV-4 Cdca8 Hmg20b1 0.725 0.620419336 0.45 0.665 0.174 ENR+CV-4 Hmg20b Pdap12 0.725 0.526391966 0.45 0.899 0.398 ENR+CV-4 Pdap1 Sub12 0.723 0.560126338 0.446 0.83 0.333 ENR+CV-4 Sub1 Atp5d3 0.723 0.548048727 0.446 0.908 0.415 ENR+CV-4 Atp5d Galk13 0.723 0.53982809 0.446 0.688 0.186 ENR+CV-4 Galk1 Fgfbp11 0.723 0.472748414 0.446 0.766 0.231 ENR+CV-4 Fgfbp1 Arl6ip1 0.722 0.763163913 0.444 0.725 0.282 ENR+CV-4 Arl6ip1 2410015M20Rik2 0.722 0.553079541 0.444 0.743 0.243 ENR+CV-4 2410015M20Rik Prmt11 0.722 0.547636331 0.444 0.766 0.256 ENR+CV-4 Prmt1 Aldh1b11 0.722 0.535950813 0.444 0.835 0.338 ENR+CV-4 Aldh1b1 Srrm11 0.722 0.526477733 0.444 0.826 0.328 ENR+CV-4 Srrm1 Mif2 0.721 0.537589281 0.442 0.922 0.499 ENR+CV-4 Mif Eif5a1 0.721 0.536312264 0.442 0.917 0.516 ENR+CV-4 Eif5a Atp5e2 0.721 0.449399589 0.442 0.963 0.665 ENR+CV-4 Atp5e Cbx31 0.72 0.624650764 0.44 0.619 0.146 ENR+CV-4 Cbx3 Pfdn11 0.719 0.571105188 0.438 0.725 0.232 ENR+CV-4 Pfdn1 Mrpl281 0.719 0.523768186 0.438 0.748 0.244 ENR+CV-4 Mrpl28 Ndufa101 0.719 0.514497454 0.438 0.761 0.256 ENR+CV-4 Ndufa10 Psma72 0.719 0.474044792 0.438 0.959 0.573 ENR+CV-4 Psma7 Hsp90ab11 0.719 0.34768932 0.438 1 0.932 ENR+CV-4 Hsp90ab1 Dek 0.718 0.522855438 0.436 0.826 0.317 ENR+CV-4 Dek Nol71 0.718 0.512547775 0.436 0.821 0.322 ENR+CV-4 Nol7 Trappc6a2 0.717 0.527000451 0.434 0.757 0.261 ENR+CV-4 Trappc6a Tacc3 0.716 0.764261261 0.432 0.528 0.08 ENR+CV-4 Tacc3 Pbk 0.716 0.615892696 0.432 0.56 0.098 ENR+CV-4 Pbk Hnrnpd1 0.716 0.565255386 0.432 0.638 0.165 ENR+CV-4 Hnrnpd Snrpd32 0.716 0.513976258 0.432 0.867 0.374 ENR+CV-4 Snrpd3 mt-Tc2 0.715 0.778396502 0.43 0.5 0.058 ENR+CV-4 mt-Tc Rny33 0.715 0.642039771 0.43 0.55 0.097 ENR+CV-4 Rny3 Add31 0.715 0.570862767 0.43 0.688 0.211 ENR+CV-4 Add3 D8Ertd738e1 0.715 0.52518644 0.43 0.702 0.22 ENR+CV-4 D8Ertd738e Anp32e1 0.715 0.492639902 0.43 0.679 0.191 ENR+CV-4 Anp32e Atp5b2 0.715 0.425036017 0.43 0.982 0.724 ENR+CV-4 Atp5b 2010107E04Rik2 0.714 0.444015425 0.428 0.977 0.667 ENR+CV-4 2010107E04Rik Hn1 0.713 0.524760229 0.426 0.867 0.395 ENR+CV-4 Hn1 Mtch21 0.713 0.503831272 0.426 0.789 0.301 ENR+CV-4 Mtch2 Cyc11 0.713 0.488752984 0.426 0.826 0.331 ENR+CV-4 Cyc1 Fuca11 0.713 0.481392149 0.426 0.711 0.22 ENR+CV-4 Fuca1 Cenpf 0.712 0.759271744 0.424 0.573 0.128 ENR+CV-4 Cenpf Rangap1 0.712 0.561114219 0.424 0.619 0.156 ENR+CV-4 Rangap1 Anp32a1 0.712 0.500905675 0.424 0.849 0.37 ENR+CV-4 Anp32a Ndufa32 0.712 0.48789893 0.424 0.876 0.391 ENR+CV-4 Ndufa3 Chchd101 0.712 0.467163032 0.424 0.807 0.307 ENR+CV-4 Chchd10 Rad23b1 0.711 0.555656866 0.422 0.647 0.181 ENR+CV-4 Rad23b Ilf21 0.711 0.543297591 0.422 0.624 0.159 ENR+CV-4 Ilf2 Sae11 0.711 0.538853645 0.422 0.679 0.204 ENR+CV-4 Sae1 Mrps121 0.711 0.519282432 0.422 0.61 0.144 ENR+CV-4 Mrps12 Rps282 0.711 0.518618509 0.422 0.817 0.333 ENR+CV-4 Rps28 Ier23 0.711 0.510282677 0.422 0.922 0.526 ENR+CV-4 Ier2 Ndufc12 0.711 0.477345452 0.422 0.881 0.475 ENR+CV-4 Ndufc1 Atp1a13 0.71 0.515422791 0.42 0.876 0.399 ENR+CV-4 Atp1a1 Gm102212 0.709 0.64227589 0.418 0.578 0.134 ENR+CV-4 Gm10221 Aqp12 0.709 0.578468857 0.418 0.601 0.146 ENR+CV-4 Aqp1 Birc5 0.709 0.565936071 0.418 0.592 0.133 ENR+CV-4 Birc5 Lmnb1 0.709 0.562933198 0.418 0.601 0.146 ENR+CV-4 Lmnb1 Sord1 0.709 0.511292798 0.418 0.661 0.19 ENR+CV-4 Sord Nudc1 0.709 0.497272443 0.418 0.633 0.167 ENR+CV-4 Nudc Hnf4a1 0.709 0.478357727 0.418 0.716 0.232 ENR+CV-4 Hnf4a Myeov22 0.709 0.449730154 0.418 0.876 0.372 ENR+CV-4 Myeov2 Pkm3 0.709 0.445718729 0.418 0.963 0.633 ENR+CV-4 Pkm Kif20b 0.708 0.718689213 0.416 0.55 0.111 ENR+CV-4 Kif20b Timm501 0.708 0.562724868 0.416 0.578 0.13 ENR+CV-4 Timm50 Mvb12a1 0.708 0.554731529 0.416 0.596 0.143 ENR+CV-4 Mvb12a Ckb1 0.708 0.510804146 0.416 0.766 0.278 ENR+CV-4 Ckb Ssrp11 0.708 0.506507721 0.416 0.72 0.245 ENR+CV-4 Ssrp1 Cs2 0.708 0.503298421 0.416 0.711 0.232 ENR+CV-4 Cs Crip12 0.708 0.471144199 0.416 0.862 0.395 ENR+CV-4 Crip1 Hmmr 0.707 0.665841267 0.414 0.528 0.092 ENR+CV-4 Hmmr Aifm11 0.707 0.513757201 0.414 0.596 0.142 ENR+CV-4 Aifm1 Psmb21 0.707 0.497633741 0.414 0.72 0.248 ENR+CV-4 Psmb2 Tmed91 0.707 0.459736838 0.414 0.67 0.194 ENR+CV-4 Tmed9 Pabpc42 0.706 0.530275564 0.412 0.628 0.172 ENR+CV-4 Pabpc4 Ap1s11 0.706 0.491848799 0.412 0.619 0.162 ENR+CV-4 Ap1s1 Ndufv11 0.706 0.474565855 0.412 0.702 0.23 ENR+CV-4 Ndufv1 Cdc1231 0.706 0.454481634 0.412 0.656 0.189 ENR+CV-4 Cdc123 Znhit11 0.705 0.538647366 0.41 0.583 0.138 ENR+CV-4 Znhit1 Tecr1 0.705 0.465936723 0.41 0.826 0.34 ENR+CV-4 Tecr Tmem2341 0.705 0.440371247 0.41 0.748 0.263 ENR+CV-4 Tmem234 Ndufab11 0.705 0.439127805 0.41 0.821 0.332 ENR+CV-4 Ndufab1 Tpx2 0.704 0.689152583 0.408 0.514 0.086 ENR+CV-4 Tpx2 Pkig1 0.704 0.584896893 0.408 0.573 0.133 ENR+CV-4 Pkig Phb1 0.704 0.524200669 0.408 0.578 0.133 ENR+CV-4 Phb Cps11 0.704 0.520139545 0.408 0.812 0.353 ENR+CV-4 Cps1 Rbm8a1 0.704 0.505343033 0.408 0.674 0.214 ENR+CV-4 Rbm8a Ndufv33 0.704 0.48806605 0.408 0.789 0.319 ENR+CV-4 Ndufv3 Slc25a12 0.704 0.448982999 0.408 0.661 0.192 ENR+CV-4 Slc25a1 Dhcr242 0.703 0.522901763 0.406 0.67 0.212 ENR+CV-4 Dhcr24 Cdca71 0.703 0.521715817 0.406 0.711 0.248 ENR+CV-4 Cdca7 Clptm11 0.703 0.51666567 0.406 0.573 0.132 ENR+CV-4 Clptm1 Abcf11 0.703 0.47080962 0.406 0.702 0.236 ENR+CV-4 Abcf1 Ugp21 0.703 0.429712242 0.406 0.619 0.162 ENR+CV-4 Ugp2 mmu-mir-62363 0.702 0.869674721 0.404 0.468 0.051 ENR+CV-4 mmu-mir-6236 Cyba1 0.702 0.524012317 0.404 0.661 0.207 ENR+CV-4 Cyba Ndufaf21 0.702 0.469278309 0.404 0.628 0.173 ENR+CV-4 Ndufaf2 Rpl33 0.702 0.366344853 0.404 0.982 0.759 ENR+CV-4 Rpl3 Immt1 0.701 0.442997866 0.402 0.697 0.23 ENR+CV-4 Immt Serf21 0.7 0.476718974 0.4 0.706 0.239 ENR+CV-4 Serf2 Eef23 0.7 0.36667656 0.4 0.991 0.845 ENR+CV-4 Eef2 Rabl61 0.699 0.490735115 0.398 0.592 0.153 ENR+CV-4 Rabl6 Grpel11 0.699 0.472747985 0.398 0.661 0.209 ENR+CV-4 Grpel1 Etfa1 0.699 0.438302028 0.398 0.725 0.254 ENR+CV-4 Etfa Ndufb71 0.699 0.436334912 0.398 0.798 0.319 ENR+CV-4 Ndufb7 Park72 0.699 0.431204796 0.398 0.885 0.425 ENR+CV-4 Park7 Serbp12 0.699 0.413645488 0.398 0.991 0.711 ENR+CV-4 Serbp1 Sars1 0.699 0.392541833 0.398 0.789 0.294 ENR+CV-4 Sars Ezh2 0.698 0.49179889 0.396 0.656 0.207 ENR+CV-4 Ezh2 Psmc41 0.698 0.488510197 0.396 0.624 0.181 ENR+CV-4 Psmc4 Mapk132 0.698 0.460229018 0.396 0.679 0.221 ENR+CV-4 Mapk13 Sfr11 0.698 0.428236196 0.396 0.642 0.188 ENR+CV-4 Sfr1 Cdc371 0.698 0.41794008 0.396 0.725 0.255 ENR+CV-4 Cdc37 Rrp11 0.698 0.370299279 0.396 0.72 0.24 ENR+CV-4 Rrp1 Cenpe 0.697 0.5594754 0.394 0.564 0.135 ENR+CV-4 Cenpe Rfc21 0.697 0.521394755 0.394 0.541 0.118 ENR+CV-4 Rfc2 Agpat51 0.697 0.477156338 0.394 0.578 0.144 ENR+CV-4 Agpat5 Snrpg3 0.697 0.475227871 0.394 0.867 0.464 ENR+CV-4 Snrpg Lad11 0.697 0.470003525 0.394 0.665 0.212 ENR+CV-4 Lad1 Mrpl461 0.697 0.459740746 0.394 0.573 0.138 ENR+CV-4 Mrpl46 Tax1bp12 0.697 0.450349166 0.394 0.899 0.457 ENR+CV-4 Tax1bp1 Scaf11 0.697 0.43556153 0.394 0.702 0.241 ENR+CV-4 Scaf11 Ywhae1 0.697 0.422199685 0.394 0.931 0.47 ENR+CV-4 Ywhae Slc25a41 0.696 0.441960168 0.392 0.766 0.308 ENR+CV-4 Slc25a4 Snw11 0.696 0.409154776 0.392 0.697 0.236 ENR+CV-4 Snw1 Ndufa51 0.696 0.406236589 0.392 0.849 0.373 ENR+CV-4 Ndufa5 Psmd121 0.695 0.463600968 0.39 0.624 0.187 ENR+CV-4 Psmd12 Rpl171 0.695 0.461322885 0.39 0.647 0.202 ENR+CV-4 Rpl17 Mrpl121 0.695 0.458885892 0.39 0.789 0.327 ENR+CV-4 Mrpl12 H2-D11 0.695 0.449059067 0.39 0.826 0.362 ENR+CV-4 H2-D1 Mapre11 0.695 0.444681807 0.39 0.624 0.183 ENR+CV-4 Mapre1 Mtdh1 0.695 0.438023366 0.39 0.766 0.305 ENR+CV-4 Mtdh Bola11 0.695 0.434011732 0.39 0.633 0.189 ENR+CV-4 Bola1 Ect2 0.694 0.542026793 0.388 0.514 0.099 ENR+CV-4 Ect2 Glrx1 0.694 0.514942064 0.388 0.564 0.143 ENR+CV-4 Glrx Rpl182 0.694 0.389984399 0.388 0.972 0.663 ENR+CV-4 Rpl18 Scd12 0.693 0.603960684 0.386 0.505 0.096 ENR+CV-4 Scd1 Cdk1 0.693 0.451972309 0.386 0.587 0.152 ENR+CV-4 Cdk1 Ppp1r1b1 0.693 0.449015105 0.386 0.725 0.27 ENR+CV-4 Ppp1r1b Sfxn11 0.693 0.43744708 0.386 0.619 0.181 ENR+CV-4 Sfxn1 Eif3h2 0.693 0.427541746 0.386 0.894 0.508 ENR+CV-4 Eif3h Snrpd21 0.693 0.424549721 0.386 0.849 0.387 ENR+CV-4 Snrpd2 Pdia41 0.693 0.410532561 0.386 0.697 0.237 ENR+CV-4 Pdia4 Dnajc81 0.692 0.48879261 0.384 0.688 0.253 ENR+CV-4 Dnajc8 Soat11 0.692 0.466173003 0.384 0.716 0.272 ENR+CV-4 Soat1 Apex11 0.692 0.446467394 0.384 0.624 0.185 ENR+CV-4 Apex1 Eef1g2 0.692 0.405879357 0.384 0.959 0.585 ENR+CV-4 Eef1g Incenp 0.691 0.601208119 0.382 0.491 0.087 ENR+CV-4 Incenp Uchl31 0.691 0.532112841 0.382 0.555 0.145 ENR+CV-4 Uchl3 Acat21 0.691 0.515288516 0.382 0.523 0.112 ENR+CV-4 Acat2 Tcof11 0.691 0.481950364 0.382 0.537 0.123 ENR+CV-4 Tcof1 Strbp1 0.691 0.450940884 0.382 0.61 0.179 ENR+CV-4 Strbp Acin11 0.691 0.447877303 0.382 0.743 0.302 ENR+CV-4 Acin1 Tyms 0.691 0.436162759 0.382 0.619 0.185 ENR+CV-4 Tyms Ybx3 0.691 0.425015384 0.382 0.706 0.252 ENR+CV-4 Ybx3 Mrpl14 0.691 0.413521008 0.382 0.679 0.234 ENR+CV-4 Mrpl14 Metap21 0.691 0.379871297 0.382 0.766 0.295 ENR+CV-4 Metap2 Tmed21 0.69 0.45723172 0.38 0.624 0.194 ENR+CV-4 Tmed2 Ubb2 0.69 0.447771969 0.38 0.945 0.737 ENR+CV-4 Ubb Aldoa2 0.69 0.431681964 0.38 0.963 0.649 ENR+CV-4 Aldoa Hnrnpu1 0.69 0.423615054 0.38 0.936 0.566 ENR+CV-4 Hnrnpu Ubqln11 0.69 0.420017195 0.38 0.61 0.177 ENR+CV-4 Ubqln1 Fth12 0.69 0.407299381 0.38 0.977 0.822 ENR+CV-4 Fth1 Lamp11 0.69 0.394363071 0.38 0.83 0.358 ENR+CV-4 Lamp1 Minos11 0.69 0.382478654 0.38 0.945 0.533 ENR+CV-4 Minos1 Slc30a21 0.689 0.645432197 0.378 0.454 0.064 ENR+CV-4 Slc30a2 Txnrd11 0.689 0.43755032 0.378 0.706 0.261 ENR+CV-4 Txnrd1 Rpl361 0.689 0.437531772 0.378 0.583 0.156 ENR+CV-4 Rpl36 Dnaja11 0.689 0.433718696 0.378 0.628 0.195 ENR+CV-4 Dnaja1 Utp3 0.689 0.425254984 0.378 0.564 0.145 ENR+CV-4 Utp3 Prim1 0.688 0.50038712 0.376 0.541 0.134 ENR+CV-4 Prim1 Rpn21 0.688 0.462434667 0.376 0.729 0.281 ENR+CV-4 Rpn2 Ywhab1 0.688 0.436761422 0.376 0.775 0.32 ENR+CV-4 Ywhab Arpc1b1 0.688 0.429200112 0.376 0.789 0.337 ENR+CV-4 Arpc1b Eif4e21 0.688 0.399667237 0.376 0.596 0.169 ENR+CV-4 Eif4e2 Stub1 0.688 0.399146024 0.376 0.688 0.242 ENR+CV-4 Stub1 Cct71 0.688 0.38280246 0.376 0.798 0.317 ENR+CV-4 Cct7 Rplp21 0.688 0.300647466 0.376 0.982 0.903 ENR+CV-4 Rplp2 Vim2 0.687 0.647484535 0.374 0.495 0.103 ENR+CV-4 Vim Aldh9a12 0.687 0.507380681 0.374 0.587 0.174 ENR+CV-4 Aldh9a1 Cks1b 0.687 0.472233625 0.374 0.541 0.133 ENR+CV-4 Cks1b Tmpo 0.687 0.471756886 0.374 0.651 0.228 ENR+CV-4 Tmpo Bzw11 0.687 0.450499601 0.374 0.794 0.37 ENR+CV-4 Bzw1 Bax1 0.687 0.430416376 0.374 0.679 0.24 ENR+CV-4 Bax Racgap1 0.686 0.576320136 0.372 0.463 0.072 ENR+CV-4 Racgap1 Acat11 0.686 0.524260928 0.372 0.555 0.152 ENR+CV-4 Acat1 Hspa14 0.686 0.442468723 0.372 0.509 0.109 ENR+CV-4 Hspa14 Hmgn5 0.686 0.41926084 0.372 0.546 0.134 ENR+CV-4 Hmgn5 Eif3l1 0.686 0.412818114 0.372 0.697 0.256 ENR+CV-4 Eif3l 0610011F06Rik1 0.686 0.398470295 0.372 0.619 0.192 ENR+CV-4 0610011F06Rik Ssr1 0.686 0.395891444 0.372 0.688 0.24 ENR+CV-4 Ssr1 Lsm5 0.685 0.461503893 0.37 0.537 0.132 ENR+CV-4 Lsm5 Slc38a21 0.685 0.448931396 0.37 0.619 0.201 ENR+CV-4 Slc38a2 Hnrnpk2 0.685 0.387755388 0.37 0.913 0.493 ENR+CV-4 Hnrnpk Rpn13 0.685 0.374525928 0.37 0.835 0.368 ENR+CV-4 Rpn1 1110004F10Rik1 0.684 0.488440002 0.368 0.615 0.209 ENR+CV-4 1110004F10Rik Glrx51 0.684 0.481875637 0.368 0.541 0.136 ENR+CV-4 Glrx5 Dnm1l1 0.684 0.419269005 0.368 0.596 0.18 ENR+CV-4 Dnm1l Psmc51 0.684 0.40838474 0.368 0.638 0.21 ENR+CV-4 Psmc5 Ube2c 0.684 0.394088235 0.368 0.661 0.224 ENR+CV-4 Ube2c Gnb21 0.684 0.392787503 0.368 0.798 0.34 ENR+CV-4 Gnb2 Ndufs21 0.684 0.391338527 0.368 0.766 0.311 ENR+CV-4 Ndufs2 Txn21 0.684 0.389405913 0.368 0.688 0.248 ENR+CV-4 Txn2 Atox12 0.684 0.383200454 0.368 0.817 0.349 ENR+CV-4 Atox1 Nap1l1 0.684 0.332941693 0.368 0.706 0.245 ENR+CV-4 Nap1l1 H2afx 0.683 0.588749735 0.366 0.523 0.133 ENR+CV-4 H2afx Ccna2 0.683 0.546191597 0.366 0.5 0.108 ENR+CV-4 Ccna2 Yme1l11 0.683 0.466398153 0.366 0.592 0.185 ENR+CV-4 Yme1l1 Ppa21 0.683 0.457064583 0.366 0.55 0.149 ENR+CV-4 Ppa2 Csde11 0.683 0.453069275 0.366 0.725 0.312 ENR+CV-4 Csde1 Ndufs62 0.683 0.364843302 0.366 0.867 0.41 ENR+CV-4 Ndufs6 Rpl142 0.683 0.304363832 0.366 0.982 0.923 ENR+CV-4 Rpl14 Esco2 0.682 0.563297615 0.364 0.459 0.075 ENR+CV-4 Esco2 Picalm 0.682 0.383090249 0.364 0.642 0.22 ENR+CV-4 Picalm Ppp1ca1 0.682 0.377801654 0.364 0.853 0.398 ENR+CV-4 Ppp1ca Ndufa121 0.682 0.36013752 0.364 0.812 0.348 ENR+CV-4 Ndufa12 Suz12 0.681 0.525225803 0.362 0.55 0.156 ENR+CV-4 Suz12 Impa11 0.681 0.457188219 0.362 0.569 0.167 ENR+CV-4 Impa1 Usp1 0.681 0.439181801 0.362 0.578 0.17 ENR+CV-4 Usp1 Rpl7l11 0.681 0.435875789 0.362 0.578 0.173 ENR+CV-4 Rpl7l1 Eif11 0.681 0.42764852 0.362 0.849 0.429 ENR+CV-4 Eif1 Sumo31 0.681 0.423602054 0.362 0.55 0.149 ENR+CV-4 Sumo3 Mrpl522 0.681 0.414509131 0.362 0.844 0.429 ENR+CV-4 Mrpl52 G3bp11 0.681 0.412770582 0.362 0.72 0.287 ENR+CV-4 G3bp1 Aamp1 0.681 0.409554132 0.362 0.578 0.169 ENR+CV-4 Aamp Mgst11 0.681 0.409091184 0.362 0.849 0.428 ENR+CV-4 Mgst1 Nap1l41 0.681 0.407769615 0.362 0.624 0.207 ENR+CV-4 Nap1l4 Atp5j2 0.681 0.400650181 0.362 0.917 0.69 ENR+CV-4 Atp5j Ndufs81 0.681 0.342833689 0.362 0.789 0.334 ENR+CV-4 Ndufs8 Calm13 0.681 0.317905921 0.362 0.995 0.872 ENR+CV-4 Calm1 Hnrnpa0 0.68 0.497457147 0.36 0.67 0.248 ENR+CV-4 Hnrnpa0 Ctsb2 0.68 0.436616519 0.36 0.775 0.353 ENR+CV-4 Ctsb Naa501 0.68 0.4225512 0.36 0.624 0.214 ENR+CV-4 Naa50 Psmd15 0.68 0.395012363 0.36 0.596 0.185 ENR+CV-4 Psmd1 Fkbp42 0.68 0.392997644 0.36 0.849 0.401 ENR+CV-4 Fkbp4 Aimp21 0.68 0.345814134 0.36 0.546 0.139 ENR+CV-4 Aimp2 Hist1h2ae 0.679 0.669743134 0.358 0.417 0.05 ENR+CV-4 Hist1h2ae Kif11 0.679 0.53354431 0.358 0.463 0.084 ENR+CV-4 Kif11 Rab5c1 0.679 0.458426524 0.358 0.509 0.121 ENR+CV-4 Rab5c Eif3b1 0.679 0.441008052 0.358 0.596 0.19 ENR+CV-4 Eif3b Ppil11 0.679 0.432546972 0.358 0.518 0.127 ENR+CV-4 Ppil1 Psmd21 0.679 0.414754014 0.358 0.564 0.161 ENR+CV-4 Psmd2 Bzw21 0.679 0.411195205 0.358 0.72 0.289 ENR+CV-4 Bzw2 Oat1 0.679 0.398524766 0.358 0.844 0.405 ENR+CV-4 Oat Hnrnpl1 0.679 0.381470976 0.358 0.702 0.269 ENR+CV-4 Hnrnpl Pebp11 0.679 0.378758007 0.358 0.812 0.358 ENR+CV-4 Pebp1 Snrpf2 0.679 0.377138937 0.358 0.794 0.343 ENR+CV-4 Snrpf Mt12 0.679 0.321424366 0.358 0.995 0.654 ENR+CV-4 Mt1 Spc24 0.678 0.538749784 0.356 0.482 0.103 ENR+CV-4 Spc24 Ctsz1 0.678 0.407610891 0.356 0.619 0.208 ENR+CV-4 Ctsz Srrt 0.678 0.390679604 0.356 0.601 0.189 ENR+CV-4 Srrt Tomm72 0.678 0.377267316 0.356 0.908 0.535 ENR+CV-4 Tomm7 Supt16 0.678 0.374746583 0.356 0.67 0.247 ENR+CV-4 Supt16 Phlda12 0.678 0.372820616 0.356 0.771 0.317 ENR+CV-4 Phlda1 Dnajc9 0.678 0.367789891 0.356 0.546 0.145 ENR+CV-4 Dnajc9 2700094K13Rik 0.678 0.361214845 0.356 0.674 0.248 ENR+CV-4 2700094K13Rik Rrm2 0.677 0.567249607 0.354 0.459 0.086 ENR+CV-4 Rrm2 Sbno11 0.677 0.406792464 0.354 0.583 0.183 ENR+CV-4 Sbno1 Lyar 0.677 0.363496725 0.354 0.587 0.179 ENR+CV-4 Lyar 2810004N23Rik1 0.677 0.358848834 0.354 0.55 0.153 ENR+CV-4 2810004N23Rik Slc25a39 0.677 0.332106275 0.354 0.665 0.239 ENR+CV-4 Slc25a39 Rfc31 0.676 0.50841338 0.352 0.505 0.126 ENR+CV-4 Rfc3 Pold21 0.676 0.504831998 0.352 0.468 0.094 ENR+CV-4 Pold2 Hjurp 0.676 0.450388798 0.352 0.578 0.183 ENR+CV-4 Hjurp Cldn71 0.676 0.386197609 0.352 0.95 0.605 ENR+CV-4 Cldn7 Akr7a51 0.676 0.338961386 0.352 0.619 0.203 ENR+CV-4 Akr7a5 Snrnp271 0.675 0.472384797 0.35 0.546 0.164 ENR+CV-4 Snrnp27 G3bp21 0.675 0.407529673 0.35 0.647 0.234 ENR+CV-4 G3bp2 Cct81 0.675 0.397739545 0.35 0.729 0.309 ENR+CV-4 Cct8 Ranbp11 0.675 0.384827397 0.35 0.894 0.523 ENR+CV-4 Ranbp1 Rnaseh2c 0.675 0.378244713 0.35 0.596 0.191 ENR+CV-4 Rnaseh2c Por2 0.675 0.374010234 0.35 0.56 0.16 ENR+CV-4 Por Lbr 0.675 0.371026739 0.35 0.606 0.197 ENR+CV-4 Lbr Pdha11 0.675 0.364468925 0.35 0.702 0.269 ENR+CV-4 Pdha1 Dhx151 0.675 0.358426136 0.35 0.683 0.261 ENR+CV-4 Dhx15 Ncl 0.675 0.330352866 0.35 0.995 0.798 ENR+CV-4 Ncl Ubc2 0.674 0.427396604 0.348 0.908 0.559 ENR+CV-4 Ubc Comt1 0.674 0.388351131 0.348 0.569 0.177 ENR+CV-4 Comt Ndufa13 0.674 0.337217893 0.348 0.807 0.367 ENR+CV-4 Ndufa1 Spc25 0.673 0.602127954 0.346 0.427 0.067 ENR+CV-4 Spc25 Tomm40 0.673 0.399390899 0.346 0.537 0.15 ENR+CV-4 Tomm40 Smc6 0.673 0.384299371 0.346 0.55 0.163 ENR+CV-4 Smc6 Aldh21 0.673 0.384069443 0.346 0.55 0.161 ENR+CV-4 Aldh2 Psmd41 0.673 0.383602955 0.346 0.619 0.217 ENR+CV-4 Psmd4 Ddb1 0.673 0.378845678 0.346 0.624 0.216 ENR+CV-4 Ddb1 Canx1 0.673 0.377972804 0.346 0.89 0.499 ENR+CV-4 Canx Gars1 0.673 0.365836801 0.346 0.665 0.249 ENR+CV-4 Gars Cyb5b1 0.673 0.362914761 0.346 0.651 0.24 ENR+CV-4 Cyb5b Ddx1 0.673 0.292593178 0.346 0.628 0.212 ENR+CV-4 Ddx1 Sgta1 0.672 0.481633307 0.344 0.5 0.125 ENR+CV-4 Sgta Fbln11 0.672 0.469946715 0.344 0.445 0.08 ENR+CV-4 Fbln1 Mfge81 0.672 0.392437381 0.344 0.569 0.175 ENR+CV-4 Mfge8 Tspo1 0.672 0.391762902 0.344 0.546 0.156 ENR+CV-4 Tspo Eif4g11 0.672 0.375141201 0.344 0.821 0.388 ENR+CV-4 Eif4g1 Bclaf1 0.672 0.363969595 0.344 0.725 0.304 ENR+CV-4 Bclaf1 St13 0.672 0.347987605 0.344 0.739 0.309 ENR+CV-4 St13 Ndufa111 0.672 0.344076857 0.344 0.72 0.298 ENR+CV-4 Ndufa11 Tspan32 0.672 0.329849744 0.344 0.683 0.259 ENR+CV-4 Tspan3 Eif2b5 0.671 0.481397833 0.342 0.445 0.083 ENR+CV-4 Eif2b5 Wbp111 0.671 0.446031616 0.342 0.514 0.139 ENR+CV-4 Wbp11 Cops61 0.671 0.39214168 0.342 0.638 0.24 ENR+CV-4 Cops6 Scd22 0.671 0.382561947 0.342 0.917 0.524 ENR+CV-4 Scd2 H3f3b1 0.671 0.376600549 0.342 0.963 0.724 ENR+CV-4 H3f3b Hopx1 0.671 0.374512746 0.342 0.725 0.306 ENR+CV-4 Hopx Snrpb21 0.671 0.368533644 0.342 0.541 0.156 ENR+CV-4 Snrpb2 Slc25a52 0.671 0.364943967 0.342 0.959 0.762 ENR+CV-4 Slc25a5 Rbm25 0.671 0.338002175 0.342 0.784 0.36 ENR+CV-4 Rbm25 Ghitm1 0.671 0.320764319 0.342 0.789 0.342 ENR+CV-4 Ghitm Epcam1 0.671 0.313293746 0.342 0.991 0.808 ENR+CV-4 Epcam Acot12 0.67 0.544185825 0.34 0.45 0.093 ENR+CV-4 Acot1 Lig1 0.67 0.496093386 0.34 0.477 0.113 ENR+CV-4 Lig1 Mrps51 0.67 0.42478924 0.34 0.509 0.137 ENR+CV-4 Mrps5 Ctsa1 0.67 0.422422193 0.34 0.537 0.155 ENR+CV-4 Ctsa Ddx391 0.67 0.398607796 0.34 0.55 0.167 ENR+CV-4 Ddx39 Dctn31 0.67 0.371238139 0.34 0.523 0.143 ENR+CV-4 Dctn3 Pcbp21 0.67 0.355994415 0.34 0.821 0.39 ENR+CV-4 Pcbp2 Sdhc1 0.67 0.352881727 0.34 0.624 0.219 ENR+CV-4 Sdhc Mcm71 0.67 0.348554368 0.34 0.528 0.145 ENR+CV-4 Mcm7 Eif1ax1 0.67 0.348506425 0.34 0.647 0.242 ENR+CV-4 Eif1ax Etfb1 0.67 0.325328403 0.34 0.803 0.374 ENR+CV-4 Etfb Rars1 0.67 0.322727933 0.34 0.711 0.283 ENR+CV-4 Rars Ldha2 0.67 0.321681419 0.34 0.977 0.683 ENR+CV-4 Ldha Nedd81 0.67 0.321469076 0.34 0.807 0.366 ENR+CV-4 Nedd8 Pet1001 0.67 0.31110172 0.34 0.573 0.177 ENR+CV-4 Pet100 Hnrnpm1 0.67 0.276863019 0.34 0.757 0.303 ENR+CV-4 Hnrnpm Casc5 0.669 0.55165573 0.338 0.427 0.072 ENR+CV-4 Casc5 Knstrn 0.669 0.521565055 0.338 0.417 0.066 ENR+CV-4 Knstrn Ncln1 0.669 0.474508215 0.338 0.472 0.111 ENR+CV-4 Ncln Nrtn1 0.669 0.465891402 0.338 0.436 0.079 ENR+CV-4 Nrtn Arhgef261 0.669 0.42612713 0.338 0.518 0.145 ENR+CV-4 Arhgef26 Timm441 0.669 0.409921028 0.338 0.514 0.14 ENR+CV-4 Timm44 Dctpp11 0.669 0.40605455 0.338 0.578 0.192 ENR+CV-4 Dctpp1 Eif4h 0.669 0.362656218 0.338 0.688 0.283 ENR+CV-4 Eif4h Stip11 0.669 0.341191781 0.338 0.661 0.256 ENR+CV-4 Stip1 Psmd71 0.669 0.33805473 0.338 0.638 0.236 ENR+CV-4 Psmd7 Dpy30 0.669 0.337090127 0.338 0.642 0.237 ENR+CV-4 Dpy30 Psma6 0.669 0.294017699 0.338 0.812 0.36 ENR+CV-4 Psma6 Kif15 0.668 0.502452402 0.336 0.445 0.088 ENR+CV-4 Kif15 Ide1 0.668 0.492597526 0.336 0.459 0.101 ENR+CV-4 Ide Carhsp11 0.668 0.385790101 0.336 0.514 0.139 ENR+CV-4 Carhsp1 Smarcc11 0.668 0.384019789 0.336 0.615 0.223 ENR+CV-4 Smarcc1 Tuba1a1 0.668 0.345153033 0.336 0.606 0.208 ENR+CV-4 Tuba1a Hes61 0.668 0.342067577 0.336 0.601 0.204 ENR+CV-4 Hes6 Mrpl331 0.668 0.338280194 0.336 0.812 0.38 ENR+CV-4 Mrpl33 Arhgdia 0.668 0.324823416 0.336 0.674 0.262 ENR+CV-4 Arhgdia Pa2g4 0.668 0.306366224 0.336 0.936 0.485 ENR+CV-4 Pa2g4 Psmb41 0.668 0.30187197 0.336 0.761 0.324 ENR+CV-4 Psmb4 Psmd141 0.668 0.286164247 0.336 0.638 0.229 ENR+CV-4 Psmd14 Psmd131 0.667 0.43333474 0.334 0.505 0.137 ENR+CV-4 Psmd13 Pin1 0.667 0.424940607 0.334 0.514 0.146 ENR+CV-4 Pin1 Npepps1 0.667 0.419532386 0.334 0.528 0.157 ENR+CV-4 Npepps Rfc1 0.667 0.414046306 0.334 0.56 0.182 ENR+CV-4 Rfc1 Cdx11 0.667 0.406475313 0.334 0.578 0.196 ENR+CV-4 Cdx1 Ccdc1071 0.667 0.399580727 0.334 0.514 0.145 ENR+CV-4 Ccdc107 Sf3b5 0.667 0.348984526 0.334 0.734 0.323 ENR+CV-4 Sf3b5 Eif3c1 0.667 0.337190612 0.334 0.862 0.445 ENR+CV-4 Eif3c Tmco11 0.667 0.330055073 0.334 0.583 0.194 ENR+CV-4 Tmco1 Uqcrh2 0.667 0.32903571 0.334 0.954 0.638 ENR+CV-4 Uqcrh Rpl311 0.667 0.305974834 0.334 0.78 0.335 ENR+CV-4 Rpl31 Ddost1 0.667 0.305101451 0.334 0.729 0.302 ENR+CV-4 Ddost Rfc4 0.666 0.383628619 0.332 0.482 0.116 ENR+CV-4 Rfc4 Ran1 0.666 0.365371443 0.332 0.817 0.435 ENR+CV-4 Ran Cdkn1b 0.666 0.35750126 0.332 0.523 0.149 ENR+CV-4 Cdkn1b Ngfrap11 0.666 0.357227422 0.332 0.587 0.197 ENR+CV-4 Ngfrap1 Pls11 0.666 0.355594668 0.332 0.573 0.19 ENR+CV-4 Pls1 Cox5a1 0.666 0.308717492 0.332 0.899 0.47 ENR+CV-4 Cox5a Nsun21 0.666 0.307194659 0.332 0.606 0.211 ENR+CV-4 Nsun2 Zfp911 0.666 0.297064785 0.332 0.592 0.2 ENR+CV-4 Zfp91 Hist1h2an 0.665 0.674177812 0.33 0.381 0.044 ENR+CV-4 Hist1h2an Cenpa 0.665 0.527590739 0.33 0.482 0.125 ENR+CV-4 Cenpa Nup85 0.665 0.478868801 0.33 0.445 0.093 ENR+CV-4 Nup85 Ncaph2 0.665 0.475306267 0.33 0.463 0.111 ENR+CV-4 Ncaph2 Tmem91 0.665 0.47132724 0.33 0.445 0.096 ENR+CV-4 Tmem9 Prpf191 0.665 0.391973919 0.33 0.56 0.183 ENR+CV-4 Prpf19 Qdpr1 0.665 0.369867851 0.33 0.528 0.158 ENR+CV-4 Qdpr Set1 0.665 0.368414125 0.33 0.775 0.37 ENR+CV-4 Set Cdh171 0.665 0.365892163 0.33 0.633 0.233 ENR+CV-4 Cdh17 Aprt1 0.665 0.346532541 0.33 0.683 0.281 ENR+CV-4 Aprt Tmem1601 0.665 0.344773789 0.33 0.592 0.205 ENR+CV-4 Tmem160 Ywhaz1 0.665 0.324580771 0.33 0.807 0.376 ENR+CV-4 Ywhaz Xrn21 0.665 0.273027946 0.33 0.67 0.259 ENR+CV-4 Xrn2 Gspt1 0.665 0.27249459 0.33 0.628 0.227 ENR+CV-4 Gspt1 Atp6v0b 0.665 0.259646371 0.33 0.61 0.207 ENR+CV-4 Atp6v0b 1700021F05Rik1 0.664 0.444897122 0.328 0.431 0.085 ENR+CV-4 1700021F05Rik Blvrb1 0.664 0.433514098 0.328 0.431 0.083 ENR+CV-4 Blvrb Psip1 0.664 0.408994978 0.328 0.491 0.131 ENR+CV-4 Psip1 Psat1 0.664 0.395386713 0.328 0.537 0.167 ENR+CV-4 Psat1 Gm102691 0.664 0.388027645 0.328 0.821 0.435 ENR+CV-4 Gm10269 Sdc4 0.664 0.346407997 0.328 0.67 0.265 ENR+CV-4 Sdc4 Polr2i1 0.664 0.340054242 0.328 0.514 0.145 ENR+CV-4 Polr2i Fus 0.664 0.33650456 0.328 0.734 0.314 ENR+CV-4 Fus Snrnp70 0.664 0.311268886 0.328 0.683 0.272 ENR+CV-4 Snrnp70 Ndufs41 0.664 0.260943989 0.328 0.739 0.312 ENR+CV-4 Ndufs4 Raly1 0.663 0.4305928 0.326 0.514 0.156 ENR+CV-4 Raly Snord1181 0.663 0.41644523 0.326 0.463 0.115 ENR+CV-4 Snord118 Lonp11 0.663 0.41193122 0.326 0.546 0.179 ENR+CV-4 Lonp1 Ipo5 0.663 0.410223746 0.326 0.537 0.174 ENR+CV-4 Ipo5 Prmt51 0.663 0.386239988 0.326 0.482 0.124 ENR+CV-4 Prmt5 Rrm1 0.663 0.375063397 0.326 0.537 0.166 ENR+CV-4 Rrm1 Tma71 0.663 0.37238474 0.326 0.606 0.229 ENR+CV-4 Tma7 Actn4 0.663 0.37189973 0.326 0.688 0.289 ENR+CV-4 Actn4 Tra2b1 0.663 0.350145825 0.326 0.628 0.237 ENR+CV-4 Tra2b Tkt2 0.663 0.347075619 0.326 0.862 0.457 ENR+CV-4 Tkt Pfdn21 0.663 0.343968577 0.326 0.491 0.127 ENR+CV-4 Pfdn2 Adipor11 0.663 0.343461264 0.326 0.583 0.201 ENR+CV-4 Adipor1 Dap31 0.663 0.336510256 0.326 0.564 0.186 ENR+CV-4 Dap3 Rpl352 0.663 0.334997231 0.326 0.917 0.712 ENR+CV-4 Rpl35 Cct51 0.663 0.319237694 0.326 0.881 0.455 ENR+CV-4 Cct5 Fam96a1 0.663 0.293036299 0.326 0.596 0.206 ENR+CV-4 Fam96a Snrpb 0.663 0.285354559 0.326 0.748 0.316 ENR+CV-4 Snrpb Nelfe 0.662 0.493177825 0.324 0.45 0.105 ENR+CV-4 Nelfe Nsmce4a 0.662 0.423956768 0.324 0.468 0.117 ENR+CV-4 Nsmce4a Lrig11 0.662 0.413099113 0.324 0.491 0.135 ENR+CV-4 Lrig1 Ap2s1 0.662 0.405875761 0.324 0.583 0.213 ENR+CV-4 Ap2s1 Nmt11 0.662 0.365337437 0.324 0.505 0.143 ENR+CV-4 Nmt1 Taf9 0.662 0.329318874 0.324 0.587 0.207 ENR+CV-4 Taf9 Tbcb1 0.662 0.325513208 0.324 0.518 0.152 ENR+CV-4 Tbcb Snd11 0.662 0.313870014 0.324 0.578 0.196 ENR+CV-4 Snd1 Gpi12 0.662 0.273270071 0.324 0.821 0.379 ENR+CV-4 Gpi1 Chchd3 0.662 0.261629411 0.324 0.587 0.197 ENR+CV-4 Chchd3 Bcas2 0.662 0.25859773 0.324 0.615 0.217 ENR+CV-4 Bcas2 Wdr45b1 0.661 0.43660642 0.322 0.436 0.093 ENR+CV-4 Wdr45b Cdca3 0.661 0.422887863 0.322 0.495 0.139 ENR+CV-4 Cdca3 Arl31 0.661 0.41129259 0.322 0.468 0.117 ENR+CV-4 Arl3 Sqle1 0.661 0.36010356 0.322 0.532 0.164 ENR+CV-4 Sqle Ndufa91 0.661 0.350362278 0.322 0.514 0.153 ENR+CV-4 Ndufa9 Thoc71 0.661 0.349914795 0.322 0.771 0.377 ENR+CV-4 Thoc7 Hadh1 0.661 0.335702471 0.322 0.711 0.31 ENR+CV-4 Hadh Rbm341 0.661 0.331056316 0.322 0.486 0.131 ENR+CV-4 Rbm34 Vps291 0.661 0.323156892 0.322 0.573 0.198 ENR+CV-4 Vps29 Rbbp4 0.661 0.318181265 0.322 0.729 0.319 ENR+CV-4 Rbbp4 Dtymk 0.661 0.309774069 0.322 0.647 0.25 ENR+CV-4 Dtymk Rbbp7 0.661 0.298779579 0.322 0.697 0.286 ENR+CV-4 Rbbp7 Gltscr21 0.661 0.296856439 0.322 0.697 0.291 ENR+CV-4 Gltscr2 Rad23a 0.66 0.436342186 0.32 0.491 0.142 ENR+CV-4 Rad23a Marcksl11 0.66 0.381017759 0.32 0.546 0.179 ENR+CV-4 Marcksl1 Glg11 0.66 0.354697737 0.32 0.482 0.128 ENR+CV-4 Glg1 H2afz 0.66 0.329041963 0.32 0.72 0.329 ENR+CV-4 H2afz Hsd17b101 0.66 0.318234529 0.32 0.583 0.2 ENR+CV-4 Hsd17b10 Cyb5r3 0.66 0.315552655 0.32 0.523 0.157 ENR+CV-4 Cyb5r3 Eif2s2 0.66 0.314523627 0.32 0.849 0.422 ENR+CV-4 Eif2s2 Hsp90b11 0.66 0.314338717 0.32 0.968 0.704 ENR+CV-4 Hsp90b1 Wdr611 0.66 0.30452697 0.32 0.587 0.207 ENR+CV-4 Wdr61 Chmp4b 0.66 0.278630038 0.32 0.615 0.226 ENR+CV-4 Chmp4b Vaultrc52 0.66 0.274522775 0.32 0.67 0.289 ENR+CV-4 Vaultrc5 Cuta 0.659 0.426885337 0.318 0.5 0.15 ENR+CV-4 Cuta Smn11 0.659 0.416343615 0.318 0.44 0.1 ENR+CV-4 Smn1 Hdac31 0.659 0.408327897 0.318 0.472 0.126 ENR+CV-4 Hdac3 Acadl1 0.659 0.38732077 0.318 0.468 0.12 ENR+CV-4 Acadl Aes1 0.659 0.352588746 0.318 0.633 0.249 ENR+CV-4 Aes Aars 0.659 0.345477055 0.318 0.509 0.15 ENR+CV-4 Aars Mapk1 0.659 0.344281155 0.318 0.523 0.162 ENR+CV-4 Mapk1 Mdh11 0.659 0.327696381 0.318 0.775 0.369 ENR+CV-4 Mdh1 Psmb51 0.659 0.325334211 0.318 0.628 0.245 ENR+CV-4 Psmb5 Suclg11 0.659 0.323715253 0.318 0.739 0.335 ENR+CV-4 Suclg1 Eif3i 0.659 0.322553597 0.318 0.872 0.454 ENR+CV-4 Eif3i Knop1 0.659 0.322148937 0.318 0.56 0.187 ENR+CV-4 Knop1 Atp5a1 0.659 0.321714912 0.318 0.963 0.609 ENR+CV-4 Atp5a1 Pgp 0.659 0.318621881 0.318 0.601 0.221 ENR+CV-4 Pgp Rab71 0.659 0.310240022 0.318 0.518 0.156 ENR+CV-4 Rab7 Ddx241 0.659 0.29598459 0.318 0.518 0.154 ENR+CV-4 Ddx24 Tubb2b1 0.658 0.490899035 0.316 0.385 0.057 ENR+CV-4 Tubb2b Gsk3b1 0.658 0.377728897 0.316 0.514 0.161 ENR+CV-4 Gsk3b Bdh11 0.658 0.366430564 0.316 0.463 0.117 ENR+CV-4 Bdh1 Utp11l1 0.658 0.358442054 0.316 0.495 0.145 ENR+CV-4 Utp11l Eno11 0.658 0.351410015 0.316 0.739 0.346 ENR+CV-4 Eno1 Lima11 0.658 0.324186996 0.316 0.628 0.246 ENR+CV-4 Lima1 D17Wsu104e1 0.658 0.320708608 0.316 0.592 0.216 ENR+CV-4 D17Wsu104e Nars1 0.658 0.303894844 0.316 0.867 0.475 ENR+CV-4 Nars Timm13 0.658 0.301216754 0.316 0.849 0.43 ENR+CV-4 Timm13 Lamtor21 0.658 0.300294284 0.316 0.569 0.195 ENR+CV-4 Lamtor2 Hspa9 0.658 0.298288996 0.316 0.83 0.425 ENR+CV-4 Hspa9 Sugt1 0.658 0.293433354 0.316 0.573 0.199 ENR+CV-4 Sugt1 Naa15 0.658 0.290739735 0.316 0.573 0.2 ENR+CV-4 Naa15 Vps35 0.658 0.289579422 0.316 0.518 0.156 ENR+CV-4 Vps35 Cd2ap1 0.658 0.25309638 0.316 0.688 0.279 ENR+CV-4 Cd2ap Ccnb2 0.657 0.506270205 0.314 0.427 0.094 ENR+CV-4 Ccnb2 Copz11 0.657 0.37751331 0.314 0.546 0.189 ENR+CV-4 Copz1 Wwp11 0.657 0.36461092 0.314 0.454 0.113 ENR+CV-4 Wwp1 Oxct1 0.657 0.325542426 0.314 0.523 0.165 ENR+CV-4 Oxct1 Gmnn 0.657 0.322284332 0.314 0.546 0.181 ENR+CV-4 Gmnn Ptms1 0.657 0.310980679 0.314 0.587 0.211 ENR+CV-4 Ptms Eif5b1 0.657 0.293408437 0.314 0.739 0.331 ENR+CV-4 Eif5b Cope1 0.657 0.268315803 0.314 0.72 0.307 ENR+CV-4 Cope Trim371 0.656 0.504794996 0.312 0.413 0.086 ENR+CV-4 Trim37 Plk1 0.656 0.484687109 0.312 0.39 0.063 ENR+CV-4 Plk1 U2af11 0.656 0.419056701 0.312 0.491 0.151 ENR+CV-4 U2af1 Hdac11 0.656 0.402622666 0.312 0.5 0.154 ENR+CV-4 Hdac1 Got21 0.656 0.401793178 0.312 0.468 0.129 ENR+CV-4 Got2 Laptm4b1 0.656 0.392263258 0.312 0.495 0.148 ENR+CV-4 Laptm4b Mpzl11 0.656 0.364314028 0.312 0.45 0.113 ENR+CV-4 Mpzl1 Rab141 0.656 0.346738193 0.312 0.523 0.171 ENR+CV-4 Rab14 Oaz12 0.656 0.337712242 0.312 0.904 0.615 ENR+CV-4 Oaz1 Calm31 0.656 0.33274162 0.312 0.693 0.301 ENR+CV-4 Calm3 Celf1 0.656 0.320510115 0.312 0.528 0.173 ENR+CV-4 Celf1 Lta4h1 0.656 0.317683966 0.312 0.537 0.178 ENR+CV-4 Lta4h Insig11 0.656 0.311534947 0.312 0.518 0.161 ENR+CV-4 Insig1 Sec61a11 0.656 0.308315291 0.312 0.619 0.24 ENR+CV-4 Sec61a1 Smarca5 0.656 0.300646863 0.312 0.628 0.245 ENR+CV-4 Smarca5 Arpc21 0.656 0.297653526 0.312 0.826 0.427 ENR+CV-4 Arpc2 Tuba1b 0.656 0.287366402 0.312 0.798 0.386 ENR+CV-4 Tuba1b Dut 0.656 0.281011027 0.312 0.628 0.245 ENR+CV-4 Dut C1qbp 0.656 0.275817378 0.312 0.734 0.325 ENR+CV-4 C1qbp Gstm51 0.656 0.272042667 0.312 0.61 0.23 ENR+CV-4 Gstm5 Clic1 0.656 0.251339406 0.312 0.679 0.276 ENR+CV-4 Clic1 RP23-45G16.5 0.655 0.525111377 0.31 0.399 0.075 ENR+CV-4 RP23-45G16.5 Lrrc591 0.655 0.422416486 0.31 0.445 0.11 ENR+CV-4 Lrrc59 Rps252 0.655 0.350670548 0.31 0.881 0.547 ENR+CV-4 Rps25 2700029M09Rik 0.655 0.344425997 0.31 0.514 0.163 ENR+CV-4 2700029M09Rik Ptges3 0.655 0.325497707 0.31 0.665 0.283 ENR+CV-4 Ptges3 Ptp4a21 0.655 0.319278718 0.31 0.734 0.339 ENR+CV-4 Ptp4a2 Capzb1 0.655 0.297157062 0.31 0.665 0.278 ENR+CV-4 Capzb Smc1a 0.655 0.285733326 0.31 0.587 0.218 ENR+CV-4 Smc1a Ndufb101 0.655 0.285449848 0.31 0.615 0.234 ENR+CV-4 Ndufb10 Fdps 0.655 0.282166933 0.31 0.683 0.287 ENR+CV-4 Fdps Phb21 0.655 0.253274434 0.31 0.693 0.286 ENR+CV-4 Phb2 Rbm471 0.654 0.399486726 0.308 0.583 0.227 ENR+CV-4 Rbm47 Fam104a1 0.654 0.377863575 0.308 0.482 0.143 ENR+CV-4 Fam104a Atp5g3 0.654 0.365539154 0.308 0.881 0.471 ENR+CV-4 Atp5g3 Pes11 0.654 0.354694951 0.308 0.468 0.129 ENR+CV-4 Pes1 Tcerg1 0.654 0.34846106 0.308 0.495 0.15 ENR+CV-4 Tcerg1 Mtf2 0.654 0.327385761 0.308 0.45 0.113 ENR+CV-4 Mtf2 Uchl5 0.654 0.320014681 0.308 0.5 0.153 ENR+CV-4 Uchl5 Eif3f1 0.654 0.298586472 0.308 0.83 0.431 ENR+CV-4 Eif3f Hook11 0.654 0.293398393 0.308 0.853 0.447 ENR+CV-4 Hook1 Vcp1 0.654 0.28900104 0.308 0.628 0.247 ENR+CV-4 Vcp Letm1 0.653 0.416450408 0.306 0.422 0.096 ENR+CV-4 Letm1 Abcf2 0.653 0.406890248 0.306 0.417 0.092 ENR+CV-4 Abcf2 Tsc22d41 0.653 0.406703039 0.306 0.431 0.103 ENR+CV-4 Tsc22d4 Ccdc124 0.653 0.388477874 0.306 0.459 0.124 ENR+CV-4 Ccdc124 Asna11 0.653 0.374130817 0.306 0.431 0.102 ENR+CV-4 Asna1 Dsg21 0.653 0.373507085 0.306 0.541 0.193 ENR+CV-4 Dsg2 Rnf187 0.653 0.370080349 0.306 0.491 0.149 ENR+CV-4 Rnf187 Pnkd1 0.653 0.359091487 0.306 0.454 0.118 ENR+CV-4 Pnkd Blmh1 0.653 0.344989542 0.306 0.454 0.118 ENR+CV-4 Blmh Aup11 0.653 0.335521837 0.306 0.514 0.165 ENR+CV-4 Aup1 Sod1 0.653 0.312546785 0.306 0.917 0.547 ENR+CV-4 Sod1 Cox171 0.653 0.294958314 0.306 0.656 0.276 ENR+CV-4 Cox17 Atp5l1 0.653 0.29075963 0.306 0.601 0.226 ENR+CV-4 Atp5l Bsg3 0.653 0.270281931 0.306 0.986 0.727 ENR+CV-4 Bsg Hadha1 0.653 0.263995424 0.306 0.638 0.258 ENR+CV-4 Hadha Slc7a5 0.652 0.501041268 0.304 0.381 0.065 ENR+CV-4 Slc7a5 Agmat1 0.652 0.464331078 0.304 0.376 0.061 ENR+CV-4 Agmat Ralgps21 0.652 0.412204816 0.304 0.417 0.092 ENR+CV-4 Ralgps2 Ssna1 0.652 0.41104223 0.304 0.445 0.116 ENR+CV-4 Ssna1 Lsm71 0.652 0.3889045 0.304 0.417 0.093 ENR+CV-4 Lsm7 Kras 0.652 0.377256728 0.304 0.454 0.123 ENR+CV-4 Kras Stmn1 0.652 0.370176616 0.304 0.472 0.135 ENR+CV-4 Stmn1 Nlrp61 0.652 0.369772904 0.304 0.495 0.154 ENR+CV-4 Nlrp6 Khdrbs11 0.652 0.344289978 0.304 0.532 0.185 ENR+CV-4 Khdrbs1 Sec31a1 0.652 0.336512699 0.304 0.518 0.172 ENR+CV-4 Sec31a Pak1ip1 0.652 0.322095467 0.304 0.518 0.171 ENR+CV-4 Pak1ip1 Gale1 0.652 0.299572437 0.304 0.518 0.167 ENR+CV-4 Gale Srsf1 0.652 0.298651007 0.304 0.5 0.152 ENR+CV-4 Srsf1 Rabac11 0.652 0.274679278 0.304 0.528 0.174 ENR+CV-4 Rabac1 Cbx5 0.652 0.273389267 0.304 0.56 0.198 ENR+CV-4 Cbx5 Hnrnpdl 0.652 0.254481355 0.304 0.661 0.267 ENR+CV-4 Hnrnpdl Sgol1 0.651 0.494512586 0.302 0.362 0.051 ENR+CV-4 Sgol1 Bex41 0.651 0.48055676 0.302 0.394 0.078 ENR+CV-4 Bex4 Chchd6 0.651 0.47199616 0.302 0.372 0.058 ENR+CV-4 Chchd6 Diap3 0.651 0.428296437 0.302 0.376 0.06 ENR+CV-4 Diap3 Psenen1 0.651 0.424658466 0.302 0.385 0.069 ENR+CV-4 Psenen Emc8 0.651 0.406808068 0.302 0.436 0.11 ENR+CV-4 Emc8 Pmvk1 0.651 0.395181641 0.302 0.422 0.099 ENR+CV-4 Pmvk Mrps91 0.651 0.363210172 0.302 0.445 0.117 ENR+CV-4 Mrps9 Samm50 0.651 0.331921143 0.302 0.482 0.144 ENR+CV-4 Samm50 Asns 0.651 0.326679794 0.302 0.638 0.27 ENR+CV-4 Asns Gsr1 0.651 0.315854328 0.302 0.532 0.182 ENR+CV-4 Gsr Bri3bp1 0.651 0.306762595 0.302 0.463 0.128 ENR+CV-4 Bri3bp Kcnq12 0.651 0.287192159 0.302 0.5 0.154 ENR+CV-4 Kcnq1 Sc4mol 0.651 0.277254499 0.302 0.592 0.227 ENR+CV-4 Sc4mol Fkbp2 0.651 0.272084012 0.302 0.592 0.229 ENR+CV-4 Fkbp2 Ptgr11 0.651 0.253972151 0.302 0.596 0.224 ENR+CV-4 Ptgr1 Acot71 0.65 0.44480374 0.3 0.399 0.083 ENR+CV-4 Acot7 Hbegf1 0.65 0.383581494 0.3 0.56 0.211 ENR+CV-4 Hbegf Puf60 0.65 0.354611462 0.3 0.486 0.149 ENR+CV-4 Puf60 M6pr1 0.65 0.347583988 0.3 0.509 0.171 ENR+CV-4 M6pr Fbp21 0.65 0.281335781 0.3 0.564 0.206 ENR+CV-4 Fbp2 Cnih4 0.65 0.254820446 0.3 0.555 0.195 ENR+CV-4 Cnih4 Amn1 0.649 0.487246076 0.298 0.372 0.064 ENR+CV-4 Amn Dgcr6 0.649 0.447758603 0.298 0.394 0.082 ENR+CV-4 Dgcr6 Hmgb3 0.649 0.430737682 0.298 0.394 0.082 ENR+CV-4 Hmgb3 Atad2 0.649 0.365116743 0.298 0.45 0.12 ENR+CV-4 Atad2 Elf32 0.649 0.35012133 0.298 0.661 0.292 ENR+CV-4 Elf3 Ilf3 0.649 0.341105762 0.298 0.454 0.125 ENR+CV-4 Ilf3 Btg11 0.649 0.328845008 0.298 0.491 0.154 ENR+CV-4 Btg1 Polr2m 0.649 0.316870425 0.298 0.55 0.203 ENR+CV-4 Polr2m Atp6v1a1 0.649 0.316281949 0.298 0.445 0.117 ENR+CV-4 Atp6v1a Timm10b1 0.649 0.308898934 0.298 0.5 0.16 ENR+CV-4 Timm10b Mrps17 0.649 0.279292265 0.298 0.509 0.164 ENR+CV-4 Mrps17 Gipc2 0.649 0.27030012 0.298 0.532 0.184 ENR+CV-4 Gipc2 Cox6c3 0.649 0.264944787 0.298 0.977 0.78 ENR+CV-4 Cox6c Ssx2ip1 0.648 0.418476953 0.296 0.404 0.091 ENR+CV-4 Ssx2ip Shmt2 0.648 0.403653756 0.296 0.463 0.139 ENR+CV-4 Shmt2 Cox191 0.648 0.348052973 0.296 0.44 0.117 ENR+CV-4 Cox19 Alkbh51 0.648 0.321180129 0.296 0.468 0.137 ENR+CV-4 Alkbh5 Pgrmc21 0.648 0.320028984 0.296 0.468 0.137 ENR+CV-4 Pgrmc2 Ppp5c 0.648 0.307659006 0.296 0.459 0.129 ENR+CV-4 Ppp5c Azin1 0.648 0.283431031 0.296 0.495 0.155 ENR+CV-4 Azin1 Krtcap2 0.648 0.257736946 0.296 0.693 0.304 ENR+CV-4 Krtcap2 Pmm1 0.647 0.512284826 0.294 0.367 0.064 ENR+CV-4 Pmm1 Poc1a 0.647 0.462857178 0.294 0.344 0.041 ENR+CV-4 Poc1a Ddx19a 0.647 0.435564391 0.294 0.39 0.079 ENR+CV-4 Ddx19a Tfrc 0.647 0.340402506 0.294 0.486 0.156 ENR+CV-4 Tfrc Hnrnpab 0.647 0.335725179 0.294 0.849 0.475 ENR+CV-4 Hnrnpab Pcm1 0.647 0.324531997 0.294 0.546 0.203 ENR+CV-4 Pcm1 Cox7c1 0.647 0.306604436 0.294 0.734 0.361 ENR+CV-4 Cox7c Snrpc1 0.647 0.305153599 0.294 0.445 0.12 ENR+CV-4 Snrpc Cnn31 0.647 0.296645683 0.294 0.583 0.229 ENR+CV-4 Cnn3 Cd811 0.647 0.282818594 0.294 0.885 0.48 ENR+CV-4 Cd81 Elof1 0.647 0.281811682 0.294 0.5 0.161 ENR+CV-4 Elof1 Tsn1 0.647 0.281552658 0.294 0.523 0.182 ENR+CV-4 Tsn Sf3b2 0.647 0.275565348 0.294 0.642 0.268 ENR+CV-4 Sf3b2 1110008F13Rik1 0.647 0.27453518 0.294 0.624 0.258 ENR+CV-4 1110008F13Rik Fam162a1 0.647 0.251895647 0.294 0.743 0.346 ENR+CV-4 Fam162a Mecr1 0.646 0.388189363 0.292 0.404 0.092 ENR+CV-4 Mecr Aqp41 0.646 0.314248957 0.292 0.436 0.115 ENR+CV-4 Aqp4 Psmb31 0.646 0.309428359 0.292 0.624 0.266 ENR+CV-4 Psmb3 Cpne31 0.646 0.289586674 0.292 0.518 0.183 ENR+CV-4 Cpne3 Hist1h1e 0.646 0.289497648 0.292 0.61 0.247 ENR+CV-4 Hist1h1e Acaa21 0.646 0.279017327 0.292 0.537 0.192 ENR+CV-4 Acaa2 Vps361 0.646 0.267004542 0.292 0.514 0.176 ENR+CV-4 Vps36 Hspa8 0.646 0.265670461 0.292 0.986 0.77 ENR+CV-4 Hspa8 Aurkb 0.645 0.429339282 0.29 0.349 0.048 ENR+CV-4 Aurkb Cryzl11 0.645 0.395189119 0.29 0.417 0.105 ENR+CV-4 Cryzl1 Rpa2 0.645 0.391936206 0.29 0.372 0.067 ENR+CV-4 Rpa2 Spata24 0.645 0.385991762 0.29 0.372 0.067 ENR+CV-4 Spata24 Eif1ad 0.645 0.380845021 0.29 0.394 0.085 ENR+CV-4 Eif1ad Gm45401 0.645 0.374922144 0.29 0.5 0.172 ENR+CV-4 Gm4540 Prkcsh1 0.645 0.321826641 0.29 0.5 0.169 ENR+CV-4 Prkcsh Xpo1 0.645 0.305477469 0.29 0.472 0.145 ENR+CV-4 Xpo1 Rnf7 0.645 0.294936033 0.29 0.537 0.198 ENR+CV-4 Rnf7 Nipsnap11 0.645 0.292274846 0.29 0.454 0.13 ENR+CV-4 Nipsnap1 Aig11 0.645 0.290184442 0.29 0.463 0.138 ENR+CV-4 Aig1 Pkn21 0.645 0.269646851 0.29 0.482 0.152 ENR+CV-4 Pkn2 Ppig 0.645 0.266779213 0.29 0.564 0.218 ENR+CV-4 Ppig Cd91 0.645 0.25913769 0.29 0.615 0.25 ENR+CV-4 Cd9 Clybl1 0.644 0.443714733 0.288 0.376 0.076 ENR+CV-4 Clybl Sigmar11 0.644 0.376193874 0.288 0.399 0.092 ENR+CV-4 Sigmar1 Dpysl21 0.644 0.363250719 0.288 0.427 0.115 ENR+CV-4 Dpysl2 Gm102631 0.644 0.346429428 0.288 0.404 0.094 ENR+CV-4 Gm10263 Hells 0.644 0.343949981 0.288 0.505 0.177 ENR+CV-4 Hells Mrps26 0.644 0.329273931 0.288 0.445 0.128 ENR+CV-4 Mrps26 Higd1a1 0.644 0.312609564 0.288 0.463 0.142 ENR+CV-4 Higd1a Zc3h15 0.644 0.293495979 0.288 0.55 0.212 ENR+CV-4 Zc3h15 Rad21 0.644 0.259092466 0.288 0.573 0.225 ENR+CV-4 Rad21 Fyttd11 0.644 0.258087343 0.288 0.495 0.166 ENR+CV-4 Fyttd1 Ckap2l 0.643 0.465135799 0.286 0.349 0.053 ENR+CV-4 Ckap2l Ckap5 0.643 0.386945088 0.286 0.422 0.113 ENR+CV-4 Ckap5 Pla2g12a1 0.643 0.327545992 0.286 0.44 0.126 ENR+CV-4 Pla2g12a Cdk2ap21 0.643 0.32640794 0.286 0.477 0.154 ENR+CV-4 Cdk2ap2 Lrpprc 0.643 0.311464662 0.286 0.427 0.113 ENR+CV-4 Lrpprc Psmd111 0.643 0.302071708 0.286 0.486 0.163 ENR+CV-4 Psmd11 Ldlr 0.643 0.284014317 0.286 0.472 0.149 ENR+CV-4 Ldlr Cotl11 0.643 0.2760333 0.286 0.596 0.243 ENR+CV-4 Cotl1 Tomm70a1 0.643 0.271025126 0.286 0.596 0.25 ENR+CV-4 Tomm70a Aimp1 0.643 0.269813445 0.286 0.606 0.25 ENR+CV-4 Aimp1 Hmgn1 0.643 0.267159815 0.286 0.899 0.526 ENR+CV-4 Hmgn1 Hsd17b121 0.643 0.263909135 0.286 0.61 0.255 ENR+CV-4 Hsd17b12 Tnpo31 0.642 0.375753898 0.284 0.404 0.099 ENR+CV-4 Tnpo3 Prelid21 0.642 0.37147467 0.284 0.431 0.122 ENR+CV-4 Prelid2 H2-Ke2 0.642 0.336246352 0.284 0.422 0.112 ENR+CV-4 H2-Ke2 Tmem54 0.642 0.325901449 0.284 0.431 0.12 ENR+CV-4 Tmem54 Limd1 0.642 0.324653572 0.284 0.399 0.093 ENR+CV-4 Limd1 Tob1 0.642 0.295380327 0.284 0.468 0.147 ENR+CV-4 Tob1 Smchd1 0.642 0.28976823 0.284 0.45 0.131 ENR+CV-4 Smchd1 Pgd1 0.642 0.278687046 0.284 0.514 0.18 ENR+CV-4 Pgd Aurkaip1 0.642 0.261691729 0.284 0.5 0.169 ENR+CV-4 Aurkaip1 Psmb11 0.642 0.254217297 0.284 0.927 0.593 ENR+CV-4 Psmb1 Cab39l 0.641 0.435081551 0.282 0.353 0.062 ENR+CV-4 Cab39l Thoc3 0.641 0.415211666 0.282 0.372 0.075 ENR+CV-4 Thoc3 Rtf1 0.641 0.385552494 0.282 0.408 0.105 ENR+CV-4 Rtf1 Dlat1 0.641 0.329664821 0.282 0.427 0.119 ENR+CV-4 Dlat Wdr431 0.641 0.323265599 0.282 0.532 0.204 ENR+CV-4 Wdr43 Rgcc1 0.641 0.321569094 0.282 0.706 0.368 ENR+CV-4 Rgcc Me21 0.641 0.318330371 0.282 0.468 0.152 ENR+CV-4 Me2 Drap11 0.641 0.300897032 0.282 0.468 0.148 ENR+CV-4 Drap1 Dera1 0.641 0.295782072 0.282 0.459 0.145 ENR+CV-4 Dera Smim20 0.641 0.279187454 0.282 0.431 0.119 ENR+CV-4 Smim20 Ube2k 0.641 0.26692081 0.282 0.482 0.159 ENR+CV-4 Ube2k Mbnl11 0.641 0.264419375 0.282 0.532 0.195 ENR+CV-4 Mbnl1 Adk 0.641 0.250804817 0.282 0.459 0.139 ENR+CV-4 Adk Aurka 0.64 0.434979796 0.28 0.335 0.045 ENR+CV-4 Aurka Ppp1r7 0.64 0.357851734 0.28 0.404 0.103 ENR+CV-4 Ppp1r7 Tspan31 0.64 0.26835933 0.28 0.459 0.141 ENR+CV-4 Tspan31 0610007P14Rik 0.64 0.268159967 0.28 0.491 0.168 ENR+CV-4 0610007P14Rik Fau 0.64 0.260614206 0.28 0.633 0.276 ENR+CV-4 Fau Sox42 0.64 0.259866123 0.28 0.766 0.367 ENR+CV-4 Sox4 Mrpl151 0.64 0.252779889 0.28 0.624 0.271 ENR+CV-4 Mrpl15 Coro1c 0.639 0.418711098 0.278 0.372 0.08 ENR+CV-4 Coro1c Rnd31 0.639 0.404849427 0.278 0.413 0.112 ENR+CV-4 Rnd3 Eif2b41 0.639 0.380142916 0.278 0.385 0.09 ENR+CV-4 Eif2b4 Yrdc1 0.639 0.377976245 0.278 0.39 0.092 ENR+CV-4 Yrdc Bub1 0.639 0.372410583 0.278 0.358 0.065 ENR+CV-4 Bub1 Hspa4l 0.639 0.356310631 0.278 0.394 0.095 ENR+CV-4 Hspa4l Elovl11 0.639 0.334923395 0.278 0.404 0.104 ENR+CV-4 Elovl1 Zfp503 0.639 0.332192694 0.278 0.39 0.089 ENR+CV-4 Zfp503 Dhrs41 0.639 0.330226 0.278 0.541 0.217 ENR+CV-4 Dhrs4 Nop14 0.639 0.320161781 0.278 0.445 0.136 ENR+CV-4 Nop14 Ppm1g1 0.639 0.318595673 0.278 0.472 0.155 ENR+CV-4 Ppm1g Dkc11 0.639 0.31256963 0.278 0.509 0.189 ENR+CV-4 Dkc1 Rab1b 0.639 0.31147767 0.278 0.422 0.117 ENR+CV-4 Rab1b Shmt11 0.639 0.293188027 0.278 0.427 0.118 ENR+CV-4 Shmt1 Fam96b1 0.639 0.277888543 0.278 0.417 0.112 ENR+CV-4 Fam96b Gins2 0.638 0.396156237 0.276 0.372 0.081 ENR+CV-4 Gins2 Plk4 0.638 0.395800506 0.276 0.335 0.048 ENR+CV-4 Plk4 Xrcc1 0.638 0.365878926 0.276 0.353 0.064 ENR+CV-4 Xrcc1 Nfia1 0.638 0.365420315 0.276 0.427 0.126 ENR+CV-4 Nfia Fam111a 0.638 0.353293738 0.276 0.353 0.064 ENR+CV-4 Fam111a Pole3 0.638 0.352143379 0.276 0.394 0.097 ENR+CV-4 Pole3 Mrto4 0.638 0.313130691 0.276 0.422 0.119 ENR+CV-4 Mrto4 Nsdhl1 0.638 0.301688834 0.276 0.39 0.093 ENR+CV-4 Nsdhl Eif4a11 0.638 0.293519513 0.276 0.803 0.481 ENR+CV-4 Eif4a1 Etf1 0.638 0.281849255 0.276 0.606 0.257 ENR+CV-4 Etf1 1110001J03Rik1 0.638 0.273807218 0.276 0.555 0.222 ENR+CV-4 1110001J03Rik Hist2h2bb 0.637 0.458322705 0.274 0.335 0.051 ENR+CV-4 Hist2h2bb Mars 0.637 0.385445323 0.274 0.394 0.102 ENR+CV-4 Mars Pisd1 0.637 0.336668131 0.274 0.431 0.131 ENR+CV-4 Pisd Cmc2 0.637 0.321446476 0.274 0.353 0.064 ENR+CV-4 Cmc2 2310036O22Rik 0.637 0.286697279 0.274 0.459 0.149 ENR+CV-4 2310036O22Rik Atp13a3 0.637 0.267453223 0.274 0.445 0.137 ENR+CV-4 Atp13a3 Fdft1 0.637 0.256228886 0.274 0.477 0.161 ENR+CV-4 Fdft1 Vdac1 0.637 0.252143759 0.274 0.67 0.308 ENR+CV-4 Vdac1 Asf1b 0.636 0.412320824 0.272 0.317 0.038 ENR+CV-4 Asf1b Rbm381 0.636 0.38500037 0.272 0.353 0.068 ENR+CV-4 Rbm38 Psmd3 0.636 0.309545626 0.272 0.431 0.129 ENR+CV-4 Psmd3 Slc6a61 0.636 0.308991754 0.272 0.427 0.126 ENR+CV-4 Slc6a6 Myb 0.636 0.304971812 0.272 0.408 0.112 ENR+CV-4 Myb Cenpw 0.636 0.277047868 0.272 0.431 0.128 ENR+CV-4 Cenpw Csnk2b 0.636 0.272457299 0.272 0.477 0.163 ENR+CV-4 Csnk2b Fam32a1 0.636 0.266005911 0.272 0.472 0.16 ENR+CV-4 Fam32a Ddx211 0.636 0.261920255 0.272 0.665 0.322 ENR+CV-4 Ddx21 Ahcyl1 0.636 0.261350959 0.272 0.486 0.171 ENR+CV-4 Ahcyl1 Axin21 0.636 0.261145253 0.272 0.564 0.232 ENR+CV-4 Axin2 Asah1 0.636 0.252155347 0.272 0.459 0.146 ENR+CV-4 Asah1 Slc16a32 0.635 0.384191345 0.27 0.394 0.105 ENR+CV-4 Slc16a3 Mpnd2 0.635 0.368868069 0.27 0.385 0.096 ENR+CV-4 Mpnd Ndufs51 0.635 0.363296538 0.27 0.427 0.132 ENR+CV-4 Ndufs5 Rdh11 0.635 0.348329524 0.27 0.372 0.084 ENR+CV-4 Rdh11 Ap2a2 0.635 0.3126178 0.27 0.385 0.094 ENR+CV-4 Ap2a2 Hdac2 0.635 0.279240452 0.27 0.477 0.168 ENR+CV-4 Hdac2 Ppie1 0.635 0.276781613 0.27 0.408 0.113 ENR+CV-4 Ppie Ppp1cb1 0.635 0.265449714 0.27 0.56 0.228 ENR+CV-4 Ppp1cb Sarnp1 0.635 0.26461051 0.27 0.482 0.169 ENR+CV-4 Sarnp Emc10 0.635 0.26367078 0.27 0.454 0.147 ENR+CV-4 Emc10 Ctbp1 0.635 0.25236991 0.27 0.459 0.149 ENR+CV-4 Ctbp1 Fads11 0.634 0.358505812 0.268 0.404 0.115 ENR+CV-4 Fads1 Rell1 0.634 0.355626005 0.268 0.353 0.072 ENR+CV-4 Rell1 Hsd17b11 0.634 0.342172731 0.268 0.372 0.085 ENR+CV-4 Hsd17b11 Nudcd3 0.634 0.331748329 0.268 0.358 0.075 ENR+CV-4 Nudcd3 Itga61 0.634 0.312724988 0.268 0.468 0.164 ENR+CV-4 Itga6 Ywhag 0.634 0.304427373 0.268 0.417 0.125 ENR+CV-4 Ywhag Polr2b 0.634 0.298278882 0.268 0.408 0.114 ENR+CV-4 Polr2b Ccz11 0.634 0.296029121 0.268 0.39 0.099 ENR+CV-4 Ccz1 Zc3h13 0.634 0.293792914 0.268 0.413 0.118 ENR+CV-4 Zc3h13 Aldh18a11 0.634 0.283718003 0.268 0.454 0.154 ENR+CV-4 Aldh18a1 Ywhah 0.634 0.282444 0.268 0.459 0.151 ENR+CV-4 Ywhah Pum2 0.634 0.272196661 0.268 0.427 0.127 ENR+CV-4 Pum2 Tspan7 0.634 0.264996807 0.268 0.431 0.132 ENR+CV-4 Tspan7 Lars22 0.634 0.256328028 0.268 0.927 0.604 ENR+CV-4 Lars2 Sgol2 0.633 0.450322004 0.266 0.312 0.038 ENR+CV-4 Sgol2 Cars 0.633 0.396678823 0.266 0.376 0.094 ENR+CV-4 Cars Ncapg 0.633 0.37222054 0.266 0.358 0.076 ENR+CV-4 Ncapg Srm1 0.633 0.321162388 0.266 0.408 0.117 ENR+CV-4 Srm Smarcd21 0.633 0.309664492 0.266 0.399 0.11 ENR+CV-4 Smarcd2 Gins1 0.633 0.306863377 0.266 0.427 0.132 ENR+CV-4 Gins1 Tipin 0.633 0.295315981 0.266 0.417 0.124 ENR+CV-4 Tipin Stt3b1 0.633 0.282817896 0.266 0.5 0.192 ENR+CV-4 Stt3b Fkbp81 0.633 0.278250257 0.266 0.505 0.19 ENR+CV-4 Fkbp8 Capns1 0.633 0.26139724 0.266 0.477 0.17 ENR+CV-4 Capns1 mt-Ta 0.632 0.52011571 0.264 0.298 0.03 ENR+CV-4 mt-Ta Bspry 0.632 0.418086977 0.264 0.339 0.065 ENR+CV-4 Bspry Ppp3r1 0.632 0.343054494 0.264 0.376 0.095 ENR+CV-4 Ppp3r1 Ddx10 0.632 0.306047969 0.264 0.381 0.095 ENR+CV-4 Ddx10 Syngr2 0.632 0.305361182 0.264 0.468 0.167 ENR+CV-4 Syngr2 Scpep11 0.632 0.29936659 0.264 0.367 0.085 ENR+CV-4 Scpep1 Nubp11 0.632 0.280538742 0.264 0.399 0.11 ENR+CV-4 Nubp1 Usp101 0.632 0.265646459 0.264 0.427 0.13 ENR+CV-4 Usp10 Cdx21 0.632 0.260363808 0.264 0.417 0.123 ENR+CV-4 Cdx2 Eif2b1 0.632 0.25757233 0.264 0.436 0.139 ENR+CV-4 Eif2b1 Ass11 0.631 0.430272833 0.262 0.312 0.044 ENR+CV-4 Ass1 Nomo1 0.631 0.30617481 0.262 0.408 0.122 ENR+CV-4 Nomo1 Iars 0.631 0.30384173 0.262 0.422 0.132 ENR+CV-4 Iars Commd4 0.631 0.296226012 0.262 0.454 0.158 ENR+CV-4 Commd4 Nans 0.631 0.286497408 0.262 0.422 0.131 ENR+CV-4 Nans Eif4e 0.631 0.265640858 0.262 0.404 0.113 ENR+CV-4 Eif4e Net11 0.631 0.264027699 0.262 0.459 0.159 ENR+CV-4 Net1 Hn1l 0.631 0.262887953 0.262 0.381 0.095 ENR+CV-4 Hn1l n-R5-8s11 0.63 0.472028508 0.26 0.312 0.044 ENR+CV-4 n-R5-8s1 Kif23 0.63 0.336091265 0.26 0.376 0.095 ENR+CV-4 Kif23 Rassf41 0.63 0.332438122 0.26 0.335 0.062 ENR+CV-4 Rassf4 Actn11 0.63 0.29816753 0.26 0.472 0.175 ENR+CV-4 Actn1 Hat1 0.63 0.266787855 0.26 0.417 0.127 ENR+CV-4 Hat1 Rps4y21 0.629 0.367340969 0.258 0.394 0.116 ENR+CV-4 Rps4y2 Ccnb1 0.629 0.330017227 0.258 0.339 0.067 ENR+CV-4 Ccnb1 Cdkn2aipnl1 0.629 0.293411053 0.258 0.394 0.113 ENR+CV-4 Cdkn2aipnl Eif2a1 0.629 0.265578565 0.258 0.468 0.171 ENR+CV-4 Eif2a Gar11 0.629 0.252312069 0.258 0.39 0.106 ENR+CV-4 Gar1 Acsl4 0.628 0.361873568 0.256 0.349 0.08 ENR+CV-4 Acsl4 Mcm5 0.628 0.36152962 0.256 0.367 0.094 ENR+CV-4 Mcm5 Rbbp81 0.628 0.337089067 0.256 0.358 0.086 ENR+CV-4 Rbbp8 Rbm22 0.628 0.327031707 0.256 0.367 0.092 ENR+CV-4 Rbm22 Hexim11 0.628 0.321477174 0.256 0.394 0.116 ENR+CV-4 Hexim1 Cetn21 0.628 0.287459197 0.256 0.404 0.122 ENR+CV-4 Cetn2 Utp14a1 0.628 0.287294189 0.256 0.417 0.134 ENR+CV-4 Utp14a Ogdh 0.628 0.271497075 0.256 0.394 0.111 ENR+CV-4 Ogdh Gtf2f2 0.628 0.269606098 0.256 0.381 0.102 ENR+CV-4 Gtf2f2 Crip2 0.627 0.468832798 0.254 0.284 0.027 ENR+CV-4 Crip2 Rfc5 0.627 0.332928657 0.254 0.349 0.079 ENR+CV-4 Rfc5 Nudt19 0.627 0.30588313 0.254 0.404 0.126 ENR+CV-4 Nudt19 Ndfip21 0.627 0.282070888 0.254 0.399 0.118 ENR+CV-4 Ndfip2 Tmprss41 0.627 0.280667597 0.254 0.422 0.136 ENR+CV-4 Tmprss4 Abhd17a1 0.627 0.262663453 0.254 0.39 0.109 ENR+CV-4 Abhd17a Yes1 0.627 0.257371906 0.254 0.394 0.115 ENR+CV-4 Yes1 Gpa331 0.627 0.256744797 0.254 0.472 0.178 ENR+CV-4 Gpa33 mt-Tq2 0.626 0.507613601 0.252 0.298 0.041 ENR+CV-4 mt-Tq Haus3 0.626 0.408491992 0.252 0.289 0.032 ENR+CV-4 Haus3 Elovl6 0.626 0.379800454 0.252 0.358 0.093 ENR+CV-4 Elovl6 Fen1 0.626 0.36493647 0.252 0.335 0.071 ENR+CV-4 Fen1 Rpa1 0.626 0.357229408 0.252 0.33 0.067 ENR+CV-4 Rpa1 Fastkd2 0.626 0.341038691 0.252 0.326 0.063 ENR+CV-4 Fastkd2 Slc29a1 0.626 0.333677875 0.252 0.367 0.097 ENR+CV-4 Slc29a1 Cenph 0.626 0.33274086 0.252 0.335 0.071 ENR+CV-4 Cenph Uaca 0.626 0.321591416 0.252 0.367 0.096 ENR+CV-4 Uaca Elovl51 0.626 0.315432295 0.252 0.353 0.084 ENR+CV-4 Elovl5 Suclg21 0.626 0.311892372 0.252 0.394 0.121 ENR+CV-4 Suclg2 Bnip31 0.626 0.310358559 0.252 0.45 0.166 ENR+CV-4 Bnip3 1-Jun 0.626 0.287709687 0.252 0.849 0.537 ENR+CV-4 Jun Ruvbl2 0.626 0.277440729 0.252 0.376 0.101 ENR+CV-4 Ruvbl2 Hmga11 0.626 0.269209705 0.252 0.367 0.094 ENR+CV-4 Hmga1 Pigt1 0.625 0.347217637 0.25 0.353 0.087 ENR+CV-4 Pigt Pold3 0.625 0.341609002 0.25 0.353 0.089 ENR+CV-4 Pold3 Mrpl38 0.625 0.300642861 0.25 0.376 0.104 ENR+CV-4 Mrpl38 Gna111 0.625 0.288473003 0.25 0.394 0.12 ENR+CV-4 Gna11 Ipo71 0.625 0.276403818 0.25 0.413 0.136 ENR+CV-4 Ipo7 Hif1a 0.625 0.252852129 0.25 0.381 0.105 ENR+CV-4 Hif1a Cep55 0.624 0.411824822 0.248 0.298 0.042 ENR+CV-4 Cep55 Lhpp1 0.624 0.368480228 0.248 0.326 0.065 ENR+CV-4 Lhpp Prps2 0.624 0.330792474 0.248 0.335 0.072 ENR+CV-4 Prps2 Dbf4 0.624 0.330519029 0.248 0.335 0.073 ENR+CV-4 Dbf4 Yif1a 0.624 0.327090787 0.248 0.339 0.077 ENR+CV-4 Yif1a Irf2bp1 0.624 0.323781201 0.248 0.33 0.068 ENR+CV-4 Irf2bp1 Ckap2 0.624 0.296999071 0.248 0.335 0.072 ENR+CV-4 Ckap2 Pdcd51 0.624 0.270689529 0.248 0.463 0.176 ENR+CV-4 Pdcd5 Cnot6 0.624 0.250235558 0.248 0.399 0.122 ENR+CV-4 Cnot6 Usp5 0.623 0.296070093 0.246 0.349 0.085 ENR+CV-4 Usp5 Szrd11 0.623 0.294557625 0.246 0.39 0.12 ENR+CV-4 Szrd1 Rapgef61 0.623 0.282129135 0.246 0.362 0.098 ENR+CV-4 Rapgef6 Khsrp 0.623 0.281588039 0.246 0.367 0.1 ENR+CV-4 Khsrp Sap30 0.623 0.274040743 0.246 0.344 0.08 ENR+CV-4 Sap30 Ergic1 0.623 0.272957798 0.246 0.417 0.141 ENR+CV-4 Ergic1 Rad50 0.623 0.264624691 0.246 0.381 0.111 ENR+CV-4 Rad50 Med101 0.623 0.255804697 0.246 0.362 0.096 ENR+CV-4 Med10 Sys1 0.623 0.250792429 0.246 0.394 0.122 ENR+CV-4 Sys1 Gps2 0.622 0.309477253 0.244 0.353 0.092 ENR+CV-4 Gps2 Asf1a 0.622 0.259245481 0.244 0.381 0.113 ENR+CV-4 Asf1a Tex10 0.622 0.250514396 0.244 0.326 0.066 ENR+CV-4 Tex10 Bub1b 0.621 0.420436517 0.242 0.289 0.04 ENR+CV-4 Bub1b B3galtl1 0.621 0.415895288 0.242 0.312 0.061 ENR+CV-4 B3galtl Gm224261 0.621 0.393583924 0.242 0.294 0.045 ENR+CV-4 Gm22426 Pigs 0.621 0.334602414 0.242 0.321 0.067 ENR+CV-4 Pigs Vrk1 0.621 0.333487514 0.242 0.335 0.079 ENR+CV-4 Vrk1 Grn1 0.621 0.325156479 0.242 0.344 0.087 ENR+CV-4 Grn Ing2 0.621 0.319572792 0.242 0.321 0.066 ENR+CV-4 Ing2 Psme3 0.621 0.296635304 0.242 0.339 0.081 ENR+CV-4 Psme3 Galm1 0.621 0.2669532 0.242 0.367 0.105 ENR+CV-4 Galm Exosc8 0.621 0.266145568 0.242 0.353 0.093 ENR+CV-4 Exosc8 Glyr1 0.621 0.257287166 0.242 0.427 0.151 ENR+CV-4 Glyr1 Ap3b1 0.621 0.252537964 0.242 0.413 0.139 ENR+CV-4 Ap3b1 Srd5a1 0.62 0.39435197 0.24 0.307 0.058 ENR+CV-4 Srd5a1 Thumpd1 0.62 0.367588858 0.24 0.335 0.081 ENR+CV-4 Thumpd1 Ift74 0.62 0.343265365 0.24 0.312 0.061 ENR+CV-4 Ift74 Cdc34 0.62 0.306463274 0.24 0.353 0.095 ENR+CV-4 Cdc34 5830418K08Rik 0.62 0.302865047 0.24 0.326 0.071 ENR+CV-4 5830418K08Rik Crot 0.62 0.282663514 0.24 0.353 0.095 ENR+CV-4 Crot Dnajb11 0.62 0.253627237 0.24 0.372 0.109 ENR+CV-4 Dnajb11 Kif4 0.619 0.347123971 0.238 0.294 0.046 ENR+CV-4 Kif4 Pde5a 0.619 0.341161587 0.238 0.312 0.063 ENR+CV-4 Pde5a Vat11 0.619 0.338434089 0.238 0.312 0.064 ENR+CV-4 Vat1 Ttc1 0.619 0.3032868 0.238 0.349 0.094 ENR+CV-4 Ttc1 Tmx2 0.619 0.290595514 0.238 0.349 0.093 ENR+CV-4 Tmx2 Eftud2 0.619 0.28894147 0.238 0.362 0.105 ENR+CV-4 Eftud2 Gtf3c2 0.618 0.274717511 0.236 0.339 0.086 ENR+CV-4 Gtf3c2 Shoc2 0.618 0.274245318 0.236 0.367 0.108 ENR+CV-4 Shoc2 Prkag1 0.618 0.272555399 0.236 0.321 0.071 ENR+CV-4 Prkag1 Ppih 0.618 0.261990744 0.236 0.349 0.094 ENR+CV-4 Ppih Tex9 0.617 0.383774176 0.234 0.28 0.039 ENR+CV-4 Tex9 Tsfm 0.617 0.30071894 0.234 0.344 0.093 ENR+CV-4 Tsfm Rpia 0.617 0.279474692 0.234 0.33 0.08 ENR+CV-4 Rpia Zfp7031 0.617 0.274955225 0.234 0.362 0.107 ENR+CV-4 Zfp703 Clic61 0.617 0.272257971 0.234 0.349 0.097 ENR+CV-4 Clic6 Cdc25a 0.617 0.263242377 0.234 0.335 0.085 ENR+CV-4 Cdc25a Pola1 0.617 0.256622112 0.234 0.339 0.087 ENR+CV-4 Pola1 Snx21 0.617 0.250007402 0.234 0.381 0.123 ENR+CV-4 Snx2 Umps 0.616 0.32148919 0.232 0.335 0.088 ENR+CV-4 Umps Mcm3 0.616 0.315931459 0.232 0.358 0.107 ENR+CV-4 Mcm3 Dhx40 0.616 0.309394901 0.232 0.326 0.08 ENR+CV-4 Dhx40 Dnaaf2 0.616 0.304305212 0.232 0.303 0.06 ENR+CV-4 Dnaaf2 Zcchc17 0.616 0.256421425 0.232 0.372 0.117 ENR+CV-4 Zcchc17 Stk11 0.616 0.250995595 0.232 0.349 0.097 ENR+CV-4 Stk11 Mrpl191 0.616 0.25063656 0.232 0.367 0.113 ENR+CV-4 Mrpl19 Snord49b1 0.615 0.369311634 0.23 0.284 0.046 ENR+CV-4 Snord49b A430005L14Rik 0.615 0.32039217 0.23 0.317 0.073 ENR+CV-4 A430005L14Rik Rtfdc1 0.615 0.308006814 0.23 0.339 0.095 ENR+CV-4 Rtfdc1 Ntmt11 0.615 0.293681918 0.23 0.321 0.077 ENR+CV-4 Ntmt1 Mogs 0.615 0.283989883 0.23 0.303 0.061 ENR+CV-4 Mogs Sephs21 0.615 0.250925623 0.23 0.399 0.14 ENR+CV-4 Sephs2 Atf32 0.614 0.358958947 0.228 0.518 0.255 ENR+CV-4 Atf3 Tceal81 0.614 0.323786018 0.228 0.353 0.107 ENR+CV-4 Tceal8 Fam98b 0.614 0.310854215 0.228 0.33 0.089 ENR+CV-4 Fam98b Brd71 0.614 0.305282135 0.228 0.367 0.119 ENR+CV-4 Brd7 Nmt2 0.614 0.294021041 0.228 0.33 0.087 ENR+CV-4 Nmt2 Dpp8 0.614 0.293236292 0.228 0.33 0.087 ENR+CV-4 Dpp8 Cenpk 0.614 0.275361044 0.228 0.289 0.051 ENR+CV-4 Cenpk Jagn1 0.614 0.274150281 0.228 0.372 0.12 ENR+CV-4 Jagn1 Stk381 0.614 0.270959938 0.228 0.335 0.09 ENR+CV-4 Stk38 Atic 0.614 0.266512734 0.228 0.381 0.129 ENR+CV-4 Atic Naa35 0.614 0.265968033 0.228 0.349 0.103 ENR+CV-4 Naa35 Gnl3l 0.614 0.260701927 0.228 0.349 0.101 ENR+CV-4 Gnl3l Hnrnpul1 0.614 0.257772384 0.228 0.367 0.119 ENR+CV-4 Hnrnpul1 D2Wsu81e 0.613 0.368401553 0.226 0.303 0.067 ENR+CV-4 D2Wsu81e Cenpp 0.613 0.317145041 0.226 0.284 0.048 ENR+CV-4 Cenpp Zak 0.613 0.309756947 0.226 0.317 0.077 ENR+CV-4 Zak Mrpl4 0.613 0.283629564 0.226 0.349 0.104 ENR+CV-4 Mrpl4 Srsf9 0.613 0.25845922 0.226 0.335 0.092 ENR+CV-4 Srsf9 Prkar2a1 0.613 0.257638718 0.226 0.367 0.12 ENR+CV-4 Prkar2a Zc3h18 0.613 0.257334768 0.226 0.353 0.106 ENR+CV-4 Zc3h18 Slc31a11 0.613 0.254220284 0.226 0.367 0.119 ENR+CV-4 Slc31a1 Mpst1 0.612 0.340138084 0.224 0.294 0.06 ENR+CV-4 Mpst Agpat1 0.612 0.322153203 0.224 0.312 0.076 ENR+CV-4 Agpat1 Cdc42se2 0.612 0.286017471 0.224 0.307 0.071 ENR+CV-4 Cdc42se2 Lss 0.612 0.284279086 0.224 0.326 0.087 ENR+CV-4 Lss Slc25a15 0.612 0.271353559 0.224 0.303 0.067 ENR+CV-4 Slc25a15 Sertad1 0.612 0.271337923 0.224 0.321 0.081 ENR+CV-4 Sertad1 Eri1 0.612 0.267068661 0.224 0.321 0.082 ENR+CV-4 Eri1 Tnfaip1 0.612 0.255671673 0.224 0.326 0.086 ENR+CV-4 Tnfaip1 Ppp3ca 0.612 0.253076048 0.224 0.339 0.097 ENR+CV-4 Ppp3ca Casp31 0.612 0.250496293 0.224 0.326 0.087 ENR+CV-4 Casp3 Gm246011 0.611 0.435601181 0.222 0.266 0.039 ENR+CV-4 Gm24601 Melk 0.611 0.377722843 0.222 0.275 0.046 ENR+CV-4 Melk Ncapg2 0.611 0.330955973 0.222 0.28 0.05 ENR+CV-4 Ncapg2 Tmed1 0.611 0.320936223 0.222 0.284 0.054 ENR+CV-4 Tmed1 Tssc4 0.611 0.299007834 0.222 0.307 0.074 ENR+CV-4 Tssc4 Slc25a13 0.611 0.284516581 0.222 0.298 0.066 ENR+CV-4 Slc25a13 Acads1 0.611 0.256787714 0.222 0.33 0.092 ENR+CV-4 Acads Plod21 0.61 0.435768294 0.22 0.261 0.037 ENR+CV-4 Plod2 Blm 0.61 0.414459228 0.22 0.252 0.029 ENR+CV-4 Blm Nuf2 0.61 0.37954463 0.22 0.266 0.041 ENR+CV-4 Nuf2 2310011J03Rik 0.61 0.302501514 0.22 0.298 0.067 ENR+CV-4 2310011J03Rik C330027C09Rik 0.61 0.287450981 0.22 0.289 0.057 ENR+CV-4 C330027C09Rik Efr3a1 0.61 0.277233886 0.22 0.344 0.106 ENR+CV-4 Efr3a Irf81 0.61 0.271948655 0.22 0.312 0.078 ENR+CV-4 Irf8 Wipi1 0.61 0.271457838 0.22 0.312 0.078 ENR+CV-4 Wipi1 Grb2 0.61 0.270873786 0.22 0.33 0.094 ENR+CV-4 Grb2 Cyp2j61 0.61 0.265117202 0.22 0.381 0.137 ENR+CV-4 Cyp2j6 Yipf1 0.61 0.251337274 0.22 0.326 0.089 ENR+CV-4 Yipf1 Kif20a 0.609 0.364371068 0.218 0.28 0.054 ENR+CV-4 Kif20a Eefsec 0.609 0.361513738 0.218 0.271 0.045 ENR+CV-4 Eefsec Shcbp1 0.609 0.340993964 0.218 0.261 0.037 ENR+CV-4 Shcbp1 Sympk 0.609 0.311329566 0.218 0.303 0.073 ENR+CV-4 Sympk Kpna3 0.609 0.303616678 0.218 0.33 0.099 ENR+CV-4 Kpna3 Gtf2e2 0.609 0.280838174 0.218 0.326 0.093 ENR+CV-4 Gtf2e2 Alcam 0.609 0.270193664 0.218 0.326 0.093 ENR+CV-4 Alcam Rad51ap1 0.608 0.351250973 0.216 0.261 0.039 ENR+CV-4 Rad51ap1 Tead21 0.608 0.311897227 0.216 0.307 0.08 ENR+CV-4 Tead2 Micu1 0.608 0.305973606 0.216 0.298 0.072 ENR+CV-4 Micu1 Asl 0.608 0.302896244 0.216 0.284 0.058 ENR+CV-4 Asl D10Wsu102e1 0.608 0.300028757 0.216 0.303 0.076 ENR+CV-4 D10Wsu102e Afg3l1 0.608 0.293809122 0.216 0.298 0.071 ENR+CV-4 Afg3l1 Prmt7 0.608 0.292948387 0.216 0.298 0.071 ENR+CV-4 Prmt7 Mtap 0.608 0.292469689 0.216 0.307 0.077 ENR+CV-4 Mtap Cited21 0.608 0.272663432 0.216 0.303 0.074 ENR+CV-4 Cited2 Srebf2 0.608 0.269659638 0.216 0.344 0.11 ENR+CV-4 Srebf2 Acp6 0.607 0.357136764 0.214 0.289 0.067 ENR+CV-4 Acp6 Kif18a 0.607 0.332108695 0.214 0.248 0.029 ENR+CV-4 Kif18a Qsox2 0.607 0.287273561 0.214 0.289 0.064 ENR+CV-4 Qsox2 Yars 0.607 0.268201161 0.214 0.326 0.094 ENR+CV-4 Yars Nob11 0.607 0.259556749 0.214 0.326 0.096 ENR+CV-4 Nob1 Lias 0.607 0.251568136 0.214 0.289 0.064 ENR+CV-4 Lias Sapcd2 0.606 0.344509264 0.212 0.243 0.027 ENR+CV-4 Sapcd2 3110082I17Rik 0.606 0.319165232 0.212 0.266 0.047 ENR+CV-4 3110082I17Rik Elovl7 0.606 0.271177344 0.212 0.298 0.074 ENR+CV-4 Elovl7 Dhrs7b 0.606 0.269370767 0.212 0.317 0.088 ENR+CV-4 Dhrs7b Clic4 0.606 0.260096064 0.212 0.294 0.07 ENR+CV-4 Clic4 Arf3 0.606 0.257913189 0.212 0.303 0.077 ENR+CV-4 Arf3 Tnfrsf19 0.606 0.255708385 0.212 0.298 0.072 ENR+CV-4 Tnfrsf19 Tcf19 0.605 0.401346154 0.21 0.252 0.038 ENR+CV-4 Tcf19 Arhgap11a 0.605 0.349102838 0.21 0.266 0.05 ENR+CV-4 Arhgap11a Apeh 0.605 0.31415317 0.21 0.28 0.06 ENR+CV-4 Apeh Exosc2 0.605 0.305886006 0.21 0.289 0.068 ENR+CV-4 Exosc2 Ipo9 0.605 0.303488268 0.21 0.28 0.06 ENR+CV-4 Ipo9 Ppp1r35 0.605 0.302479141 0.21 0.266 0.048 ENR+CV-4 Ppp1r35 Camta11 0.605 0.266391661 0.21 0.28 0.059 ENR+CV-4 Camta1 Senp1 0.605 0.261566805 0.21 0.289 0.068 ENR+CV-4 Senp1 Prpf31 0.605 0.257009663 0.21 0.307 0.083 ENR+CV-4 Prpf31 Snrnp25 0.605 0.253226085 0.21 0.289 0.067 ENR+CV-4 Snrnp25 Gcdh 0.604 0.36156399 0.208 0.261 0.048 ENR+CV-4 Gcdh Ptpro 0.604 0.352918684 0.208 0.261 0.047 ENR+CV-4 Ptpro Tst1 0.604 0.301813014 0.208 0.275 0.059 ENR+CV-4 Tst Ankrd101 0.604 0.291383813 0.208 0.303 0.083 ENR+CV-4 Ankrd10 Nvl 0.604 0.28641588 0.208 0.298 0.078 ENR+CV-4 Nvl Coro2a 0.604 0.261692037 0.208 0.28 0.061 ENR+CV-4 Coro2a Cpox1 0.604 0.259814646 0.208 0.326 0.1 ENR+CV-4 Cpox Hist1h1d1 0.604 0.252042307 0.208 0.326 0.1 ENR+CV-4 Hist1h1d Trip13 0.603 0.302790032 0.206 0.248 0.036 ENR+CV-4 Trip13 Ncapd2 0.603 0.301622055 0.206 0.275 0.059 ENR+CV-4 Ncapd2 Zdhhc16 0.603 0.281306104 0.206 0.28 0.064 ENR+CV-4 Zdhhc16 Ythdf1 0.603 0.280808703 0.206 0.275 0.058 ENR+CV-4 Ythdf1 9-Sep 0.603 0.25856948 0.206 0.275 0.058 ENR+CV-4 9-Sep Crlf11 0.602 0.324599888 0.204 0.243 0.034 ENR+CV-4 Crlf1 Wdr76 0.602 0.29817531 0.204 0.252 0.042 ENR+CV-4 Wdr76 Slc35a4 0.602 0.277903123 0.204 0.275 0.063 ENR+CV-4 Slc35a4 Tdg 0.601 0.307606777 0.202 0.252 0.044 ENR+CV-4 Tdg Ssbp4 0.601 0.29747273 0.202 0.275 0.063 ENR+CV-4 Ssbp4 Ndc1 0.601 0.272287224 0.202 0.252 0.044 ENR+CV-4 Ndc1 Mtfp11 0.601 0.271952175 0.202 0.266 0.057 ENR+CV-4 Mtfp1 Aqr 0.601 0.266211331 0.202 0.307 0.093 ENR+CV-4 Aqr Anln 0.601 0.263897525 0.202 0.266 0.054 ENR+CV-4 Anln Mrpl49 0.601 0.250560827 0.202 0.294 0.079 ENR+CV-4 Mrpl49 Tmem120a 0.601 0.250542084 0.202 0.275 0.062 ENR+CV-4 Tmem120a Olfm41 0.81 1.226911976 0.62 0.862 0.273 ENR-1 Olfm4 Cps12 0.783 0.788114568 0.566 0.922 0.343 ENR-1 Cps1 Fabp2 0.743 0.511011373 0.486 0.9 0.383 ENR-1 Fabp2 Pigr 0.738 0.610489813 0.476 0.929 0.497 ENR-1 Pigr Gm51604 0.736 0.614479498 0.472 0.81 0.282 ENR-1 Gm5160 Gm94932 0.734 0.581927207 0.468 0.848 0.339 ENR-1 Gm9493 Clca41 0.732 0.746235305 0.464 0.851 0.436 ENR-1 Clca4 Ccl25 0.73 0.580549634 0.46 0.74 0.226 ENR-1 Ccl25 Npm11 0.727 0.459468514 0.454 0.985 0.74 ENR-1 Npm1 Hspd1 0.723 0.530228945 0.446 0.929 0.488 ENR-1 Hspd1 Otc 0.721 0.645007147 0.442 0.628 0.154 ENR-1 Otc Gm10260 0.712 0.542083966 0.424 0.736 0.26 ENR-1 Gm10260 Gm4968 0.711 0.540868382 0.422 0.706 0.232 ENR-1 Gm4968 Rpl42 0.711 0.330994832 0.422 1 0.938 ENR-1 Rpl4 Hook12 0.706 0.479315331 0.412 0.892 0.442 ENR-1 Hook1 Lgals43 0.706 0.378396697 0.412 0.989 0.797 ENR-1 Lgals4 Aldh1b12 0.705 0.491175323 0.41 0.81 0.335 ENR-1 Aldh1b1 Rpsa-ps10 0.702 0.475830688 0.404 0.662 0.198 ENR-1 Rpsa-ps10 C1qbp1 0.702 0.432385739 0.404 0.803 0.318 ENR-1 C1qbp Plcb3 0.7 0.579716423 0.4 0.632 0.188 ENR-1 Plcb3 Rps2-ps10 0.699 0.537995138 0.398 0.599 0.152 ENR-1 Rps2-ps10 Amica11 0.699 0.448912034 0.398 0.725 0.256 ENR-1 Amica1 Eef1b22 0.698 0.345420178 0.396 0.996 0.882 ENR-1 Eef1b2 Phgr14 0.697 0.41170045 0.394 0.87 0.419 ENR-1 Phgr1 Pycard 0.696 0.473739525 0.392 0.736 0.276 ENR-1 Pycard Gsto1 0.695 0.432865357 0.39 0.803 0.345 ENR-1 Gsto1 Rps61 0.694 0.464066021 0.388 0.855 0.431 ENR-1 Rps6 Gnb2l11 0.694 0.321098814 0.388 0.993 0.92 ENR-1 Gnb2l1 Gm5619 0.693 0.498968076 0.386 0.572 0.139 ENR-1 Gm5619 Mt2 0.692 0.430955838 0.384 0.933 0.509 ENR-1 Mt2 Ncl1 0.692 0.382552891 0.384 0.993 0.796 ENR-1 Ncl Lsm3 0.69 0.454639507 0.38 0.602 0.176 ENR-1 Lsm3 Rpl13-ps3 0.688 0.425179545 0.376 0.74 0.287 ENR-1 Rpl13-ps3 Hspe1 0.687 0.432319145 0.374 0.918 0.532 ENR-1 Hspe1 Rps3a11 0.687 0.307529405 0.374 0.996 0.883 ENR-1 Rps3a1 Mki671 0.686 0.560040298 0.372 0.691 0.299 ENR-1 Mki67 Rpl9-ps1 0.686 0.418515475 0.372 0.599 0.169 ENR-1 Rpl9-ps1 Rpsa 0.685 0.395225063 0.37 0.963 0.631 ENR-1 Rpsa Myb1 0.683 0.561335579 0.366 0.491 0.105 ENR-1 Myb Gm87303 0.683 0.353463848 0.366 0.967 0.716 ENR-1 Gm8730 Rps111 0.682 0.330472403 0.364 0.993 0.874 ENR-1 Rps11 Gm65762 0.681 0.431941937 0.362 0.788 0.368 ENR-1 Gm6576 Ppia2 0.681 0.409660487 0.362 0.877 0.49 ENR-1 Ppia Lbr1 0.68 0.499493887 0.36 0.595 0.194 ENR-1 Lbr Sfpq 0.679 0.379030203 0.358 0.725 0.288 ENR-1 Sfpq Gmnn1 0.678 0.529686811 0.356 0.565 0.177 ENR-1 Gmnn Gm5786 0.678 0.447990342 0.356 0.587 0.181 ENR-1 Gm5786 Ldha3 0.678 0.375459293 0.356 0.97 0.681 ENR-1 Ldha Hsp90ab12 0.677 0.298716487 0.354 0.996 0.931 ENR-1 Hsp90ab1 Gm7808 0.675 0.378422191 0.35 0.628 0.213 ENR-1 Gm7808 Ivns1abp 0.674 0.402223109 0.348 0.777 0.376 ENR-1 Ivns1abp Rpa3 0.673 0.4066077 0.346 0.677 0.279 ENR-1 Rpa3 Gstt2 0.672 0.490324512 0.344 0.498 0.127 ENR-1 Gstt2 Rpl121 0.672 0.422347108 0.344 0.673 0.269 ENR-1 Rpl12 Csrp2 0.672 0.421135636 0.344 0.565 0.179 ENR-1 Csrp2 Pa2g41 0.672 0.417996373 0.344 0.855 0.485 ENR-1 Pa2g4 Anp32b 0.672 0.402906637 0.344 0.829 0.435 ENR-1 Anp32b Tomm51 0.672 0.40230326 0.344 0.677 0.274 ENR-1 Tomm5 Atp5a11 0.672 0.36600291 0.344 0.948 0.606 ENR-1 Atp5a1 Rps10-ps11 0.672 0.352878057 0.344 0.888 0.477 ENR-1 Rps10-ps1 Rpl21-ps4 0.671 0.418847992 0.342 0.572 0.178 ENR-1 Rpl21-ps4 AI747448 0.67 0.652552706 0.34 0.454 0.097 ENR-1 AI747448 Gm8225 0.67 0.401330178 0.34 0.602 0.205 ENR-1 Gm8225 Hspa91 0.67 0.400450086 0.34 0.825 0.421 ENR-1 Hspa9 Rpl10-ps32 0.67 0.347414958 0.34 0.706 0.289 ENR-1 Rpl10-ps3 Pcbp1 0.67 0.345300966 0.34 0.743 0.312 ENR-1 Pcbp1 Hspa81 0.67 0.317339776 0.34 0.985 0.768 ENR-1 Hspa8 Tuba1b1 0.669 0.429958101 0.338 0.77 0.384 ENR-1 Tuba1b Fgfbp12 0.668 0.452645497 0.336 0.617 0.233 ENR-1 Fgfbp1 Xist3 0.668 0.397245425 0.336 0.922 0.668 ENR-1 Xist Sdc41 0.668 0.369889255 0.336 0.665 0.262 ENR-1 Sdc4 Gm81861 0.668 0.362123452 0.336 0.651 0.245 ENR-1 Gm8186 Slc25a53 0.668 0.341986244 0.336 0.981 0.759 ENR-1 Slc25a5 Tm4sf20 0.668 0.338504883 0.336 0.818 0.402 ENR-1 Tm4sf20 Mt13 0.668 0.28320989 0.336 0.974 0.652 ENR-1 Mt1 BX465866.1 0.667 0.433915498 0.334 0.487 0.118 ENR-1 BX465866.1 Fus1 0.667 0.356180534 0.334 0.725 0.311 ENR-1 Fus Gm102754 0.667 0.344343909 0.334 0.855 0.464 ENR-1 Gm10275 Pgk1 0.666 0.435093852 0.332 0.554 0.183 ENR-1 Pgk1 Ndufs7 0.665 0.348635098 0.33 0.688 0.29 ENR-1 Ndufs7 Gm64721 0.664 0.374146183 0.328 0.695 0.298 ENR-1 Gm6472 Slc12a21 0.664 0.364531809 0.328 0.881 0.491 ENR-1 Slc12a2 Atp5b3 0.664 0.330332862 0.328 0.97 0.722 ENR-1 Atp5b Rps71 0.664 0.301876888 0.328 0.97 0.801 ENR-1 Rps7 Smc3 0.663 0.40819151 0.326 0.572 0.204 ENR-1 Smc3 Mif3 0.663 0.36948123 0.326 0.877 0.497 ENR-1 Mif Top2a1 0.662 0.506413829 0.324 0.665 0.318 ENR-1 Top2a Eif4b 0.662 0.36240463 0.324 0.721 0.332 ENR-1 Eif4b Snrpd11 0.662 0.358486456 0.324 0.743 0.347 ENR-1 Snrpd1 Cdca72 0.662 0.3575881 0.324 0.639 0.247 ENR-1 Cdca7 Nop58 0.661 0.345033957 0.322 0.773 0.376 ENR-1 Nop58 Hnrnpa2b11 0.661 0.319002237 0.322 0.959 0.717 ENR-1 Hnrnpa2b1 Sri 0.66 0.326372167 0.32 0.643 0.255 ENR-1 Sri Tkt3 0.66 0.322378661 0.32 0.862 0.453 ENR-1 Tkt Gm8444 0.659 0.359255972 0.318 0.543 0.178 ENR-1 Gm8444 Banf11 0.659 0.33622482 0.318 0.818 0.427 ENR-1 Banf1 Hmgb21 0.658 0.423978338 0.316 0.836 0.479 ENR-1 Hmgb2 Sae12 0.657 0.410209832 0.314 0.561 0.205 ENR-1 Sae1 Eprs 0.657 0.334116667 0.314 0.68 0.296 ENR-1 Eprs Tubb4b1 0.656 0.45617908 0.312 0.77 0.422 ENR-1 Tubb4b Cct6a 0.656 0.371029052 0.312 0.755 0.38 ENR-1 Cct6a Myh9 0.656 0.348453619 0.312 0.762 0.382 ENR-1 Myh9 Mgam 0.655 0.366801804 0.31 0.539 0.185 ENR-1 Mgam Ppp1r1b2 0.655 0.324269294 0.31 0.654 0.269 ENR-1 Ppp1r1b Vdac11 0.655 0.323905033 0.31 0.691 0.303 ENR-1 Vdac1 Rps27a1 0.655 0.31406595 0.31 0.792 0.404 ENR-1 Rps27a Aqp42 0.654 0.483930711 0.308 0.439 0.112 ENR-1 Aqp4 Isx 0.654 0.449974563 0.308 0.398 0.071 ENR-1 Isx Smc41 0.654 0.4227726 0.308 0.617 0.268 ENR-1 Smc4 Rpl7a4 0.654 0.312469507 0.308 0.918 0.587 ENR-1 Rpl7a Crip13 0.654 0.269382773 0.308 0.818 0.393 ENR-1 Crip1 Gm98431 0.654 0.25822927 0.308 0.981 0.784 ENR-1 Gm9843 Gm21957 0.653 0.368238886 0.306 0.461 0.119 ENR-1 Gm21957 Eno12 0.653 0.339219386 0.306 0.721 0.343 ENR-1 Eno1 Ndufb5 0.653 0.31354239 0.306 0.796 0.406 ENR-1 Ndufb5 Rpl101 0.653 0.310938354 0.306 0.639 0.259 ENR-1 Rpl10 Rps23 0.653 0.261191332 0.306 0.993 0.932 ENR-1 Rps2 Rps26-ps1 0.652 0.283947704 0.304 0.58 0.212 ENR-1 Rps26-ps1 Snhg1 0.651 0.326347079 0.302 0.74 0.367 ENR-1 Snhg1 Rp91 0.651 0.313872741 0.302 0.569 0.214 ENR-1 Rp9 Rpl13a-ps11 0.651 0.303074859 0.302 0.721 0.34 ENR-1 Rpl13a-ps1 Cetn3 0.651 0.267908334 0.302 0.632 0.257 ENR-1 Cetn3 Nasp 0.65 0.343166728 0.3 0.595 0.244 ENR-1 Nasp Mrpl18 0.65 0.333886645 0.3 0.61 0.257 ENR-1 Mrpl18 Btf31 0.65 0.330101253 0.3 0.807 0.444 ENR-1 Btf3 Ndufc2 0.65 0.294977597 0.3 0.84 0.488 ENR-1 Ndufc2 2810417H13Rik1 0.649 0.441318779 0.298 0.572 0.237 ENR-1 2810417H13Rik Serbp13 0.649 0.308088704 0.298 0.955 0.71 ENR-1 Serbp1 Anxa41 0.649 0.273304253 0.298 0.907 0.567 ENR-1 Anxa4 Hjurp1 0.648 0.326033972 0.296 0.52 0.182 ENR-1 Hjurp Cct3 0.648 0.320941303 0.296 0.706 0.341 ENR-1 Cct3 Rad211 0.648 0.288329432 0.296 0.576 0.222 ENR-1 Rad21 Lgals9 0.648 0.271388134 0.296 0.621 0.253 ENR-1 Lgals9 Rpl222 0.648 0.259854933 0.296 0.974 0.784 ENR-1 Rpl22 Eef24 0.648 0.257394821 0.296 0.974 0.845 ENR-1 Eef2 Eif4ebp1 0.647 0.354843341 0.294 0.539 0.206 ENR-1 Eif4ebp1 Ccnd11 0.647 0.352833112 0.294 0.513 0.181 ENR-1 Ccnd1 Nap1l11 0.647 0.344971346 0.294 0.595 0.246 ENR-1 Nap1l1 Gm16519 0.647 0.339888997 0.294 0.409 0.09 ENR-1 Gm16519 Pgp1 0.647 0.3240671 0.294 0.561 0.22 ENR-1 Pgp Gpx2 0.647 0.287687416 0.294 0.967 0.73 ENR-1 Gpx2 Hnf4a2 0.646 0.320348152 0.292 0.584 0.233 ENR-1 Hnf4a Srsf31 0.646 0.306726302 0.292 0.848 0.476 ENR-1 Srsf3 Ehf1 0.646 0.301988942 0.292 0.695 0.32 ENR-1 Ehf Gm10704 0.646 0.287726976 0.292 0.513 0.171 ENR-1 Gm10704 Cdca81 0.645 0.38096075 0.29 0.476 0.153 ENR-1 Cdca8 Shmt21 0.645 0.365979259 0.29 0.457 0.136 ENR-1 Shmt2 Usp11 0.645 0.35681899 0.29 0.498 0.17 ENR-1 Usp1 Dut1 0.645 0.342085578 0.29 0.584 0.244 ENR-1 Dut Rpl15 0.645 0.328011524 0.29 0.565 0.224 ENR-1 Rpl15 Sdhd 0.645 0.316089911 0.29 0.688 0.324 ENR-1 Sdhd Dnajc2 0.645 0.315913549 0.29 0.599 0.255 ENR-1 Dnajc2 Ranbp12 0.645 0.291501672 0.29 0.885 0.52 ENR-1 Ranbp1 Cyc12 0.645 0.289124485 0.29 0.703 0.333 ENR-1 Cyc1 Txn11 0.645 0.258663712 0.29 0.97 0.742 ENR-1 Txn1 Gm9396 0.644 0.319678558 0.288 0.442 0.119 ENR-1 Gm9396 Nucks11 0.644 0.27441388 0.288 0.677 0.309 ENR-1 Nucks1 Rgcc2 0.643 0.383057267 0.286 0.688 0.365 ENR-1 Rgcc Pcna 0.643 0.349800646 0.286 0.625 0.284 ENR-1 Pcna Cct21 0.643 0.286296153 0.286 0.788 0.407 ENR-1 Cct2 Rrm11 0.642 0.420118982 0.284 0.48 0.166 ENR-1 Rrm1 Cct4 0.642 0.299091989 0.284 0.725 0.366 ENR-1 Cct4 Ckb2 0.642 0.289101867 0.284 0.636 0.28 ENR-1 Ckb Tspan82 0.642 0.288455293 0.284 0.896 0.58 ENR-1 Tspan8 Rpl310 0.642 0.253576604 0.284 0.981 0.757 ENR-1 Rpl3 Oat2 0.642 0.253190029 0.284 0.803 0.403 ENR-1 Oat Kpnb1 0.642 0.251126694 0.284 0.58 0.229 ENR-1 Kpnb1 Gm20594 0.641 0.427031535 0.282 0.48 0.161 ENR-1 Gm20594 Eif3e1 0.641 0.275593267 0.282 0.729 0.364 ENR-1 Eif3e Sdha 0.641 0.267501367 0.282 0.599 0.253 ENR-1 Sdha G3bp12 0.641 0.2625822 0.282 0.651 0.287 ENR-1 G3bp1 Zfp36l21 0.64 0.403068788 0.28 0.424 0.122 ENR-1 Zfp36l2 Ewsr1 0.64 0.346328646 0.28 0.543 0.219 ENR-1 Ewsr1 Lsm51 0.64 0.335376399 0.28 0.442 0.132 ENR-1 Lsm5 Zfp292 0.64 0.319066818 0.28 0.55 0.226 ENR-1 Zfp292 Pfkl1 0.64 0.312465906 0.28 0.491 0.171 ENR-1 Pfkl Prdx4 0.64 0.300581795 0.28 0.569 0.234 ENR-1 Prdx4 Idh3b 0.64 0.291613703 0.28 0.543 0.212 ENR-1 Idh3b Sdhb1 0.64 0.278080313 0.28 0.758 0.383 ENR-1 Sdhb Baz1b 0.64 0.272217475 0.28 0.55 0.216 ENR-1 Baz1b Naca1 0.64 0.260990617 0.28 0.952 0.69 ENR-1 Naca Uqcrfs1 0.64 0.259735004 0.28 0.695 0.332 ENR-1 Uqcrfs1 Dhx9 0.64 0.257751695 0.28 0.625 0.267 ENR-1 Dhx9 Idh3g 0.639 0.296611246 0.278 0.517 0.192 ENR-1 Idh3g Ssb 0.639 0.281741475 0.278 0.836 0.477 ENR-1 Ssb Hnrnpab1 0.639 0.261403714 0.278 0.84 0.472 ENR-1 Hnrnpab Nolc1 0.638 0.306214591 0.276 0.532 0.211 ENR-1 Nolc1 Cnbp1 0.638 0.289047293 0.276 0.87 0.576 ENR-1 Cnbp Tmbim4 0.638 0.269731981 0.276 0.569 0.23 ENR-1 Tmbim4 Ybx31 0.638 0.252539707 0.276 0.602 0.253 ENR-1 Ybx3 Fh1 0.637 0.323621581 0.274 0.498 0.188 ENR-1 Fh1 Cbx51 0.637 0.289384623 0.274 0.52 0.196 ENR-1 Cbx5 Srsf6 0.637 0.270063014 0.274 0.628 0.285 ENR-1 Srsf6 Rpl18a1 0.637 0.260388942 0.274 0.978 0.762 ENR-1 Rpl18a Trap1 0.636 0.315986561 0.272 0.457 0.151 ENR-1 Trap1 Gmds 0.636 0.313941446 0.272 0.584 0.258 ENR-1 Gmds Phb22 0.636 0.305145739 0.272 0.617 0.286 ENR-1 Phb2 Bzw22 0.636 0.300870805 0.272 0.628 0.289 ENR-1 Bzw2 Naa502 0.636 0.272737394 0.272 0.539 0.214 ENR-1 Naa50 Mrpl42 0.636 0.254389379 0.272 0.68 0.324 ENR-1 Mrpl42 Gdi2 0.636 0.250755394 0.272 0.699 0.347 ENR-1 Gdi2 Gm4204 0.635 0.308685191 0.27 0.42 0.123 ENR-1 Gm4204 Slc20a1 0.635 0.293038821 0.27 0.45 0.141 ENR-1 Slc20a1 Lyar1 0.635 0.289249614 0.27 0.491 0.18 ENR-1 Lyar Mrpl13 0.635 0.267662755 0.27 0.572 0.249 ENR-1 Mrpl13 Pnn 0.635 0.254946844 0.27 0.558 0.231 ENR-1 Pnn Ndufb111 0.635 0.252808048 0.27 0.807 0.457 ENR-1 Ndufb11 Cdca31 0.634 0.459009033 0.268 0.428 0.139 ENR-1 Cdca3 Hist1h1e1 0.634 0.398016565 0.268 0.55 0.247 ENR-1 Hist1h1e Ifngr1 0.634 0.370040438 0.268 0.465 0.168 ENR-1 Ifngr1 Mcm72 0.634 0.369013081 0.268 0.439 0.146 ENR-1 Mcm7 Pck2 0.634 0.330423604 0.268 0.435 0.137 ENR-1 Pck2 Gm12728 0.634 0.301848003 0.268 0.472 0.161 ENR-1 Gm12728 Tomm20 0.634 0.282951476 0.268 0.628 0.295 ENR-1 Tomm20 Thyn1 0.634 0.269786332 0.268 0.457 0.154 ENR-1 Thyn1 Pdss1 0.633 0.394521786 0.266 0.387 0.103 ENR-1 Pdss1 Nlrp62 0.633 0.353986297 0.266 0.45 0.153 ENR-1 Nlrp6 Ipo51 0.633 0.277911794 0.266 0.483 0.173 ENR-1 Ipo5 Mrps28 0.633 0.257911504 0.266 0.461 0.154 ENR-1 Mrps28 Rbbp71 0.633 0.255611373 0.266 0.625 0.286 ENR-1 Rbbp7 Dek1 0.633 0.252701943 0.266 0.665 0.32 ENR-1 Dek Tpr 0.633 0.250504124 0.266 0.688 0.338 ENR-1 Tpr Ceacam1 0.632 0.356260706 0.264 0.387 0.1 ENR-1 Ceacam1 Tfam 0.632 0.318779299 0.264 0.428 0.137 ENR-1 Tfam Clic62 0.632 0.316359452 0.264 0.375 0.093 ENR-1 Clic6 Psat11 0.632 0.29919317 0.264 0.468 0.167 ENR-1 Psat1 Ddx39b 0.632 0.279836241 0.264 0.595 0.268 ENR-1 Ddx39b Dtymk1 0.631 0.265083873 0.262 0.572 0.25 ENR-1 Dtymk Prdx6 0.631 0.252793667 0.262 0.762 0.405 ENR-1 Prdx6 Pla2g4a 0.63 0.443345474 0.26 0.335 0.063 ENR-1 Pla2g4a Tstd1 0.63 0.424007975 0.26 0.361 0.082 ENR-1 Tstd1 Cluh 0.63 0.331570871 0.26 0.431 0.142 ENR-1 Cluh Cdk11 0.63 0.326736265 0.26 0.45 0.155 ENR-1 Cdk1 Cotl12 0.63 0.267261676 0.26 0.558 0.242 ENR-1 Cotl1 Syncrip 0.63 0.256960384 0.26 0.532 0.219 ENR-1 Syncrip Mybbp1a1 0.63 0.255358253 0.26 0.535 0.223 ENR-1 Mybbp1a Cenpe1 0.629 0.424400928 0.258 0.416 0.138 ENR-1 Cenpe Tsix 0.629 0.354774907 0.258 0.372 0.094 ENR-1 Tsix Gm10073 0.629 0.291463462 0.258 0.42 0.131 ENR-1 Gm10073 Alad 0.629 0.290141073 0.258 0.472 0.176 ENR-1 Alad Pcna-ps2 0.628 0.376617835 0.256 0.394 0.116 ENR-1 Pcna-ps2 Slc35a3 0.628 0.314092412 0.256 0.398 0.12 ENR-1 Slc35a3 Orc5 0.627 0.315965573 0.254 0.576 0.272 ENR-1 Orc5 Uhrf1 0.626 0.261594985 0.252 0.398 0.12 ENR-1 Uhrf1 Ptbp1 0.626 0.255468863 0.252 0.476 0.181 ENR-1 Ptbp1 Rps3a3 0.626 0.252704803 0.252 0.487 0.187 ENR-1 Rps3a3 Smc21 0.625 0.417543003 0.25 0.446 0.171 ENR-1 Smc2 Zbtb38 0.625 0.389531928 0.25 0.349 0.087 ENR-1 Zbtb38 Ifi30 0.625 0.252448471 0.25 0.424 0.143 ENR-1 Ifi30 Hat11 0.624 0.366105231 0.248 0.394 0.125 ENR-1 Hat1 Farsb 0.624 0.352945644 0.248 0.413 0.14 ENR-1 Farsb Mrps22 0.624 0.334874923 0.248 0.394 0.125 ENR-1 Mrps22 Mthfd2 0.624 0.30998256 0.248 0.409 0.136 ENR-1 Mthfd2 Orc6 0.624 0.29631237 0.248 0.431 0.153 ENR-1 Orc6 Taf15 0.624 0.287430524 0.248 0.457 0.173 ENR-1 Taf15 Lmnb11 0.624 0.273240544 0.248 0.431 0.15 ENR-1 Lmnb1 2410004N09Rik 0.624 0.273161599 0.248 0.442 0.158 ENR-1 2410004N09Rik Smchd11 0.623 0.340895957 0.246 0.398 0.131 ENR-1 Smchd1 Gm16477 0.623 0.322625249 0.246 0.327 0.065 ENR-1 Gm16477 Tmem70 0.623 0.319533005 0.246 0.409 0.14 ENR-1 Tmem70 Mcm6 0.623 0.316644108 0.246 0.424 0.15 ENR-1 Mcm6 Kcne3 0.622 0.399945438 0.244 0.335 0.076 ENR-1 Kcne3 Ube2c1 0.622 0.386105811 0.244 0.502 0.227 ENR-1 Ube2c Dnmt1 0.622 0.265218687 0.244 0.424 0.147 ENR-1 Dnmt1 Dnajc91 0.621 0.305095217 0.242 0.416 0.148 ENR-1 Dnajc9 Gm23061 0.621 0.294862203 0.242 0.353 0.091 ENR-1 Gm23061 Nudcd2 0.621 0.265061999 0.242 0.476 0.193 ENR-1 Nudcd2 Prim11 0.62 0.329141152 0.24 0.398 0.137 ENR-1 Prim1 Atic1 0.62 0.31749315 0.24 0.387 0.126 ENR-1 Atic Eps8l3 0.62 0.277593248 0.24 0.387 0.122 ENR-1 Eps8l3 2700029M09Rik1 0.62 0.272732307 0.24 0.435 0.164 ENR-1 2700029M09Rik Mrpl47 0.62 0.255591746 0.24 0.379 0.117 ENR-1 Mrpl47 Naa38 0.62 0.254939564 0.24 0.465 0.186 ENR-1 Naa38 Lgr51 0.619 0.304444276 0.238 0.439 0.17 ENR-1 Lgr5 Cftr1 0.619 0.282925861 0.238 0.405 0.141 ENR-1 Cftr Kcnq13 0.619 0.259810417 0.238 0.424 0.154 ENR-1 Kcnq1 Tpx21 0.618 0.416123253 0.236 0.338 0.091 ENR-1 Tpx2 Aldh9a13 0.618 0.267660465 0.236 0.446 0.177 ENR-1 Aldh9a1 Cldn15 0.618 0.260919111 0.236 0.435 0.164 ENR-1 Cldn15 Nudt191 0.618 0.258782806 0.236 0.383 0.124 ENR-1 Nudt19 Hist1h1b1 0.617 0.398288984 0.234 0.413 0.16 ENR-1 Hist1h1b Ppp1r14d 0.617 0.340373465 0.234 0.375 0.12 ENR-1 Ppp1r14d Cth 0.617 0.337156072 0.234 0.379 0.123 ENR-1 Cth Shmt12 0.617 0.305092778 0.234 0.372 0.118 ENR-1 Shmt1 Atad3a1 0.617 0.277127157 0.234 0.413 0.15 ENR-1 Atad3a Gm15013 0.617 0.263283977 0.234 0.342 0.087 ENR-1 Gm15013 Ddx392 0.617 0.258776088 0.234 0.435 0.169 ENR-1 Ddx39 Tardbp 0.617 0.251972117 0.234 0.472 0.198 ENR-1 Tardbp Hells1 0.616 0.311683278 0.232 0.442 0.177 ENR-1 Hells Mpp6 0.616 0.27534406 0.232 0.353 0.102 ENR-1 Mpp6 Ccna21 0.615 0.36865724 0.23 0.357 0.111 ENR-1 Ccna2 Gm1123 0.615 0.294352836 0.23 0.368 0.114 ENR-1 Gm1123 Gm26384 0.615 0.289628944 0.23 0.32 0.074 ENR-1 Gm26384 Ces2e 0.615 0.264393442 0.23 0.361 0.107 ENR-1 Ces2e Cenpw1 0.615 0.254500541 0.23 0.383 0.127 ENR-1 Cenpw Mcm2 0.614 0.300638904 0.228 0.342 0.098 ENR-1 Mcm2 Ppif 0.614 0.274205035 0.228 0.338 0.093 ENR-1 Ppif Nudt21 0.613 0.277498277 0.226 0.383 0.132 ENR-1 Nudt21 Sfxn12 0.613 0.257158425 0.226 0.446 0.185 ENR-1 Sfxn1 AC102758.1 0.612 0.314790527 0.224 0.297 0.06 ENR-1 AC102758.1 Mrpl192 0.612 0.281890511 0.224 0.353 0.111 ENR-1 Mrpl19 Zfp326 0.612 0.279228361 0.224 0.349 0.107 ENR-1 Zfp326 Whsc1 0.611 0.273424152 0.222 0.383 0.137 ENR-1 Whsc1 Bdh12 0.611 0.264436491 0.222 0.361 0.119 ENR-1 Bdh1 Tk1 0.61 0.404265379 0.22 0.305 0.076 ENR-1 Tk1 Mcm51 0.61 0.321610611 0.22 0.327 0.093 ENR-1 Mcm5 4-Sep 0.61 0.311020966 0.22 0.323 0.091 ENR-1 4-Sep Noxo1 0.61 0.308469986 0.22 0.331 0.094 ENR-1 Noxo1 Cks2 0.61 0.270850368 0.22 0.372 0.129 ENR-1 Cks2 Mlxipl 0.61 0.265959441 0.22 0.368 0.123 ENR-1 Mlxipl Spc241 0.609 0.266983333 0.218 0.342 0.106 ENR-1 Spc24 Usp102 0.608 0.270835083 0.216 0.368 0.13 ENR-1 Usp10 Tyms1 0.607 0.291261675 0.214 0.431 0.19 ENR-1 Tyms Rad501 0.607 0.272187207 0.214 0.342 0.111 ENR-1 Rad50 Gm5277 0.607 0.265545355 0.214 0.32 0.09 ENR-1 Gm5277 Ppip5k2 0.607 0.256774763 0.214 0.368 0.132 ENR-1 Ppip5k2 Kif151 0.606 0.359126054 0.212 0.316 0.091 ENR-1 Kif15 Kif231 0.606 0.341872716 0.212 0.32 0.095 ENR-1 Kif23 Ncapg1 0.606 0.283457176 0.212 0.301 0.076 ENR-1 Ncapg Larp1 0.606 0.259656167 0.212 0.327 0.099 ENR-1 Larp1 Topbp1 0.605 0.333514036 0.21 0.32 0.096 ENR-1 Topbp1 Pbk1 0.605 0.303729342 0.21 0.331 0.104 ENR-1 Pbk Atf5 0.605 0.29322935 0.21 0.335 0.105 ENR-1 Atf5 Aadac 0.605 0.278947227 0.21 0.283 0.061 ENR-1 Aadac Igfbp4 0.605 0.252429489 0.21 0.368 0.135 ENR-1 Igfbp4 Suclg22 0.604 0.28045907 0.208 0.349 0.121 ENR-1 Suclg2 Iars1 0.604 0.253578975 0.208 0.361 0.132 ENR-1 Iars Kcnn4 0.603 0.337667044 0.206 0.264 0.05 ENR-1 Kcnn4 Kif20b1 0.603 0.328995429 0.206 0.338 0.118 ENR-1 Kif20b Vdr 0.603 0.316247425 0.206 0.301 0.082 ENR-1 Vdr Pvrl3 0.603 0.273691265 0.206 0.375 0.148 ENR-1 Pvrl3 Stat6 0.603 0.268186966 0.206 0.346 0.121 ENR-1 Stat6 Mrps31 0.603 0.266483653 0.206 0.338 0.114 ENR-1 Mrps31 Wwp12 0.602 0.291033289 0.204 0.335 0.116 ENR-1 Wwp1 1190007I07Rik 0.602 0.282890167 0.204 0.327 0.107 ENR-1 1190007I07Rik Fut8 0.602 0.25580908 0.204 0.327 0.105 ENR-1 Fut8 Hist1h1d2 0.601 0.347949629 0.202 0.312 0.099 ENR-1 Hist1h1d Lgals44 0.699 0.501826029 0.398 0.935 0.778 ENR-2 Lgals4 Olfm42 0.691 0.866124588 0.382 0.596 0.237 ENR-2 Olfm4 mt-Co13 0.689 0.473587407 0.378 0.984 0.906 ENR-2 mt-Co1 mt-Nd53 0.674 0.495547814 0.348 0.931 0.82 ENR-2 mt-Nd5 Mt21 0.667 0.53344477 0.334 0.74 0.483 ENR-2 Mt2 Phgr15 0.663 0.641090421 0.326 0.653 0.394 ENR-2 Phgr1 Fabp21 0.658 0.554010839 0.316 0.63 0.358 ENR-2 Fabp2 Ldha4 0.655 0.469817439 0.31 0.842 0.663 ENR-2 Ldha Gm98432 0.655 0.429905094 0.31 0.86 0.778 ENR-2 Gm9843 mt-Nd43 0.655 0.427437692 0.31 0.936 0.854 ENR-2 mt-Nd4 Gm87304 0.654 0.484944949 0.308 0.817 0.709 ENR-2 Gm8730 Mt14 0.649 0.336854409 0.298 0.851 0.627 ENR-2 Mt1 Eef1b23 0.643 0.355242681 0.286 0.928 0.878 ENR-2 Eef1b2 Cps13 0.64 0.631577696 0.28 0.572 0.327 ENR-2 Cps1 Pigr1 0.639 0.515270596 0.278 0.67 0.484 ENR-2 Pigr Gm94933 0.634 0.679133467 0.268 0.527 0.327 ENR-2 Gm9493 Aldoa3 0.611 0.302710337 0.222 0.781 0.634 ENR-2 Aldoa Gm102601 0.608 0.623963105 0.216 0.422 0.252 ENR-2 Gm10260 Rps72 0.607 0.29763812 0.214 0.852 0.8 ENR-2 Rps7 Ccl251 0.605 0.610584751 0.21 0.403 0.216 ENR-2 Ccl25 Gm51605 0.601 0.594103232 0.202 0.437 0.278 ENR-2 Gm5160 Aldob 0.848 1.623037231 0.696 0.892 0.414 ENR-3 Aldob Fabp12 0.845 2.384427893 0.69 0.789 0.187 ENR-3 Fabp1 Fabp22 0.817 1.388857472 0.634 0.865 0.364 ENR-3 Fabp2 Prap1 0.815 1.655418071 0.63 0.771 0.215 ENR-3 Prap1 Mt15 0.81 1.023983132 0.62 0.962 0.639 ENR-3 Mt1 Sis 0.788 1.764132223 0.576 0.695 0.17 ENR-3 Sis Mt22 0.784 0.934407414 0.568 0.892 0.495 ENR-3 Mt2 Lgals45 0.773 0.667785349 0.546 0.97 0.79 ENR-3 Lgals4 Phgr16 0.77 0.937737335 0.54 0.833 0.403 ENR-3 Phgr1 2210404O07Rik 0.745 1.228859113 0.49 0.677 0.25 ENR-3 2210404O07Rik Ldha5 0.72 0.581090664 0.44 0.952 0.67 ENR-3 Ldha mt-Co14 0.718 0.495052223 0.436 0.99 0.913 ENR-3 mt-Co1 Ccl252 0.711 1.056012878 0.422 0.602 0.216 ENR-3 Ccl25 mt-Nd22 0.707 0.425689812 0.414 0.99 0.922 ENR-3 mt-Nd2 Reg1 0.706 2.261530152 0.412 0.448 0.045 ENR-3 Reg1 Adh1 0.699 1.181060248 0.398 0.538 0.167 ENR-3 Adh1 mt-Nd44 0.689 0.432937052 0.378 0.968 0.86 ENR-3 mt-Nd4 Apoa1 0.677 1.597349307 0.354 0.388 0.038 ENR-3 Apoa1 Khk 0.676 1.099938046 0.352 0.46 0.132 ENR-3 Khk Crip14 0.674 0.637244586 0.348 0.695 0.386 ENR-3 Crip1 Olfm43 0.673 0.651208536 0.346 0.614 0.271 ENR-3 Olfm4 Gm98433 0.672 0.432324038 0.344 0.9 0.783 ENR-3 Gm9843 Pigr2 0.671 0.558387269 0.342 0.747 0.495 ENR-3 Pigr mt-Nd54 0.671 0.413011431 0.342 0.944 0.829 ENR-3 mt-Nd5 Gm94934 0.667 0.640979807 0.334 0.633 0.337 ENR-3 Gm9493 Dak 0.662 1.060434569 0.324 0.43 0.127 ENR-3 Dak Txn12 0.66 0.399287767 0.32 0.894 0.739 ENR-3 Txn1 Gsta1 0.659 1.284957561 0.318 0.394 0.083 ENR-3 Gsta1 Pycard1 0.657 0.699920387 0.314 0.55 0.273 ENR-3 Pycard Spink3 0.653 1.201322069 0.306 0.329 0.024 ENR-3 Spink3 Tm4sf201 0.651 0.692000575 0.302 0.635 0.401 ENR-3 Tm4sf20 Ces2e1 0.65 0.948245183 0.3 0.384 0.094 ENR-3 Ces2e 2200002D01Rik 0.65 0.773089545 0.3 0.494 0.216 ENR-3 2200002D01Rik Apoa4 0.647 1.447596801 0.294 0.319 0.027 ENR-3 Apoa4 Gm87305 0.643 0.383652378 0.286 0.855 0.716 ENR-3 Gm8730 Aldoa4 0.642 0.38898651 0.284 0.839 0.644 ENR-3 Aldoa Oat3 0.636 0.637382252 0.272 0.612 0.403 ENR-3 Oat mt-Co33 0.635 0.49603252 0.27 0.667 0.451 ENR-3 mt-Co3 Slc5a11 0.634 0.937974442 0.268 0.39 0.143 ENR-3 Slc5a1 Eno13 0.634 0.552498148 0.268 0.576 0.341 ENR-3 Eno1 Apoc3 0.633 1.228218134 0.266 0.285 0.02 ENR-3 Apoc3 Uqcrq3 0.631 0.333356592 0.262 0.902 0.751 ENR-3 Uqcrq Gm64722 0.63 0.525151863 0.26 0.534 0.296 ENR-3 Gm6472 Atpif1 0.629 0.330177413 0.258 0.892 0.79 ENR-3 Atpif1 Rps112 0.629 0.2836447 0.258 0.942 0.874 ENR-3 Rps11 Dbi4 0.627 0.376348252 0.254 0.914 0.816 ENR-3 Dbi Tpi14 0.627 0.342440983 0.254 0.789 0.579 ENR-3 Tpi1 Mttp 0.624 0.847934898 0.248 0.331 0.094 ENR-3 Mttp Mgam1 0.623 0.777260509 0.246 0.406 0.182 ENR-3 Mgam Cps14 0.623 0.42542916 0.246 0.59 0.349 ENR-3 Cps1 Gsto11 0.622 0.508334376 0.244 0.552 0.348 ENR-3 Gsto1 AI7474481 0.621 0.801846827 0.242 0.331 0.093 ENR-3 AI747448 Leap2 0.62 1.106124032 0.24 0.261 0.022 ENR-3 Leap2 Cox7b2 0.62 0.340366475 0.24 0.843 0.717 ENR-3 Cox7b Rps62 0.619 0.41840331 0.238 0.622 0.434 ENR-3 Rps6 Cyb5 0.616 0.583760239 0.232 0.544 0.375 ENR-3 Cyb5 Cyp4f14 0.614 0.951089623 0.228 0.255 0.029 ENR-3 Cyp4f14 Rbp2 0.614 0.926216412 0.228 0.249 0.023 ENR-3 Rbp2 Cox6b12 0.612 0.300429863 0.224 0.865 0.714 ENR-3 Cox6b1 Sult1b1 0.61 0.933386812 0.22 0.255 0.038 ENR-3 Sult1b1 Chchd102 0.608 0.556228058 0.216 0.49 0.31 ENR-3 Chchd10 Gpi13 0.608 0.452768762 0.216 0.56 0.38 ENR-3 Gpi1 Rps10-ps12 0.608 0.397633043 0.216 0.639 0.482 ENR-3 Rps10-ps1 2010001M06Rik 0.607 0.745550688 0.214 0.285 0.076 ENR-3 2010001M06Rik Gm51606 0.607 0.447997513 0.214 0.496 0.288 ENR-3 Gm5160 Mif4 0.607 0.338131266 0.214 0.681 0.499 ENR-3 Mif Gm102602 0.606 0.484237543 0.212 0.458 0.266 ENR-3 Gm10260 Slc25a54 0.605 0.263160706 0.21 0.855 0.762 ENR-3 Slc25a5 AA467197 0.603 0.951083532 0.206 0.247 0.043 ENR-3 AA467197 Maoa 0.603 0.828195852 0.206 0.285 0.087 ENR-3 Maoa Sult1d1 0.603 0.639520744 0.206 0.333 0.131 ENR-3 Sult1d1 St3gal4 0.602 0.784461899 0.204 0.233 0.031 ENR-3 St3gal4 Aadac1 0.602 0.759046337 0.204 0.255 0.054 ENR-3 Aadac Otc1 0.602 0.582354235 0.204 0.353 0.159 ENR-3 Otc Lypd8 0.602 0.529117096 0.204 0.48 0.31 ENR-3 Lypd8 Rps2-ps101 0.601 0.555761639 0.202 0.351 0.156 ENR-3 Rps2-ps10 Tubb4b2 0.601 0.396518633 0.202 0.586 0.424 ENR-3 Tubb4b Spink45 0.874 1.424394711 0.748 0.994 0.746 ENR-4 Spink4 Clps7 0.777 0.995852459 0.554 0.897 0.453 ENR-4 Clps AY7611846 0.766 1.284747632 0.532 0.817 0.361 ENR-4 AY761184 Gm152996 0.753 1.236197823 0.506 0.699 0.246 ENR-4 Gm15299 Defa244 0.748 0.673622825 0.496 0.998 0.892 ENR-4 Defa24 Defa176 0.711 0.43840216 0.422 0.992 0.708 ENR-4 Defa17 Tff36 0.707 0.573615826 0.414 0.968 0.676 ENR-4 Tff3 Fabp23 0.684 0.576616061 0.368 0.707 0.37 ENR-4 Fabp2 Guca2a6 0.683 0.673396863 0.366 0.727 0.396 ENR-4 Guca2a Defa266 0.682 0.764814463 0.364 0.626 0.276 ENR-4 Defa26 Agr25 0.681 0.722478851 0.362 0.756 0.47 ENR-4 Agr2 Gm148517 0.677 0.329003996 0.354 0.831 0.443 ENR-4 Gm14851 Lgals46 0.662 0.378296127 0.324 0.94 0.789 ENR-4 Lgals4 Mt16 0.66 0.344607346 0.32 0.899 0.639 ENR-4 Mt1 Phgr17 0.659 0.571894559 0.318 0.691 0.41 ENR-4 Phgr1 Olfm44 0.655 0.547471041 0.31 0.582 0.266 ENR-4 Olfm4 Ldha6 0.655 0.34310918 0.31 0.899 0.67 ENR-4 Ldha Fcgbp4 0.653 0.993083849 0.306 0.489 0.208 ENR-4 Fcgbp Mt23 0.647 0.415319225 0.294 0.77 0.499 ENR-4 Mt2 Klk1 0.632 1.036249612 0.264 0.297 0.034 ENR-4 Klk1 Gm94935 0.63 0.517195173 0.26 0.562 0.338 ENR-4 Gm9493 Prap11 0.625 0.419327727 0.25 0.489 0.235 ENR-4 Prap1 Gm98434 0.625 0.302627001 0.25 0.885 0.782 ENR-4 Gm9843 Gm87306 0.62 0.320970268 0.24 0.849 0.713 ENR-4 Gm8730 Gm11231 0.619 0.77980094 0.238 0.331 0.101 ENR-4 Gm1123 Aldob1 0.617 0.259787204 0.234 0.631 0.433 ENR-4 Aldob Rps63 0.611 0.415852365 0.222 0.598 0.433 ENR-4 Rps6 2210404O07Rik1 0.609 0.463037112 0.218 0.464 0.265 ENR-4 2210404O07Rik Guca2b 0.608 0.596105667 0.216 0.349 0.135 ENR-4 Guca2b Pigr3 0.604 0.332644186 0.208 0.674 0.498 ENR-4 Pigr Ifitm14 0.728 1.266514055 0.456 0.661 0.271 ENR+CD-1 Ifitm1 S100a115 0.717 1.04296412 0.434 0.701 0.397 ENR+CD-1 S100a11 Clu8 0.704 1.164798896 0.408 0.568 0.183 ENR+CD-1 Clu Ifitm34 0.695 0.868364303 0.39 0.705 0.453 ENR+CD-1 Ifitm3 Tmsb101 0.69 0.580472869 0.38 0.863 0.725 ENR+CD-1 Tmsb10 Mmp77 0.678 0.402919101 0.356 0.893 0.512 ENR+CD-1 Mmp7 D17H6S56E-54 0.677 0.931920895 0.354 0.651 0.413 ENR+CD-1 D17H6S56E-5 S100a64 0.676 1.118626018 0.352 0.627 0.349 ENR+CD-1 S100a6 Tmsb4x1 0.676 0.544945699 0.352 0.92 0.848 ENR+CD-1 Tmsb4x Thbs14 0.667 0.905834032 0.334 0.541 0.242 ENR+CD-1 Thbs1 Prdx11 0.658 0.401091653 0.316 0.931 0.876 ENR+CD-1 Prdx1 Rdh10 0.653 1.038867978 0.306 0.41 0.123 ENR+CD-1 Rdh10 Lrrc581 0.651 0.52230821 0.302 0.712 0.538 ENR+CD-1 Lrrc58 Cfi 0.65 0.955406446 0.3 0.43 0.141 ENR+CD-1 Cfi S100a10 0.637 0.657620654 0.274 0.634 0.463 ENR+CD-1 S100a10 Cd24a4 0.633 0.438901983 0.266 0.773 0.62 ENR+CD-1 Cd24a Ctsl2 0.632 0.776789752 0.264 0.474 0.247 ENR+CD-1 Ctsl Cldn43 0.63 0.668353449 0.26 0.533 0.312 ENR+CD-1 Cldn4 Krt7 0.628 0.670919893 0.256 0.526 0.323 ENR+CD-1 Krt7 Gpx1 0.627 0.433965819 0.254 0.741 0.615 ENR+CD-1 Gpx1 Hsp90aa12 0.621 0.482215686 0.242 0.678 0.545 ENR+CD-1 Hsp90aa1 Tpt14 0.617 0.300455932 0.234 0.878 0.747 ENR+CD-1 Tpt1 Myl12a 0.61 0.521781165 0.22 0.55 0.393 ENR+CD-1 Myl12a Kitl 0.605 0.774167138 0.21 0.328 0.128 ENR+CD-1 Kitl Cxadr 0.605 0.654634603 0.21 0.383 0.19 ENR+CD-1 Cxadr Myl12b1 0.605 0.429834038 0.21 0.598 0.454 ENR+CD-1 Myl12b Fxyd34 0.605 0.427737169 0.21 0.56 0.381 ENR+CD-1 Fxyd3 Sbspon 0.603 0.808834309 0.206 0.253 0.049 ENR+CD-1 Sbspon Chgb6 0.845 0.840330017 0.69 0.965 0.418 ENR+CD-2 Chgb Sct8 0.821 1.235777954 0.642 0.844 0.235 ENR+CD-2 Sct Defa37 0.803 0.802828958 0.606 0.962 0.387 ENR+CD-2 Defa3 Ang47 0.797 0.730641799 0.594 0.974 0.446 ENR+CD-2 Ang4 Mmp78 0.796 0.773345323 0.592 0.977 0.492 ENR+CD-2 Mmp7 Gm152846 0.79 0.631388586 0.58 0.998 0.691 ENR+CD-2 Gm15284 Lyz17 0.788 0.600947747 0.576 0.995 0.654 ENR+CD-2 Lyz1 Itln17 0.786 0.651103542 0.572 0.998 0.743 ENR+CD-2 Itln1 Defa217 0.783 0.776202788 0.566 0.884 0.339 ENR+CD-2 Defa21 Defa227 0.782 0.765089831 0.564 0.863 0.306 ENR+CD-2 Defa22 Defa-rs17 0.777 0.663665047 0.554 0.95 0.427 ENR+CD-2 Defa-rs1 Defa177 0.766 0.594762162 0.532 1 0.705 ENR+CD-2 Defa17 Gm153157 0.752 0.703363896 0.504 0.816 0.287 ENR+CD-2 Gm15315 Tff37 0.746 0.567941882 0.492 0.982 0.672 ENR+CD-2 Tff3 Defa245 0.742 0.474196376 0.484 1 0.891 ENR+CD-2 Defa24 Gm148518 0.739 0.446583792 0.478 0.894 0.433 ENR+CD-2 Gm14851 Clu9 0.734 0.965368487 0.468 0.64 0.164 ENR+CD-2 Clu Ifitm15 0.728 0.783309944 0.456 0.708 0.255 ENR+CD-2 Ifitm1 Cck4 0.721 1.020507077 0.442 0.65 0.224 ENR+CD-2 Cck S100a65 0.717 0.711435596 0.434 0.731 0.328 ENR+CD-2 S100a6 Gcg3 0.711 1.006429421 0.422 0.565 0.149 ENR+CD-2 Gcg Fxyd35 0.71 0.726447178 0.42 0.734 0.354 ENR+CD-2 Fxyd3 Reg3b4 0.706 0.801648267 0.412 0.603 0.195 ENR+CD-2 Reg3b Thbs15 0.706 0.796785646 0.412 0.636 0.222 ENR+CD-2 Thbs1 AY7611857 0.704 0.551190274 0.408 0.76 0.329 ENR+CD-2 AY761185 Chga4 0.7 0.679396712 0.4 0.592 0.185 ENR+CD-2 Chga Mptx21 0.696 0.754335025 0.392 0.545 0.144 ENR+CD-2 Mptx2 S100a116 0.693 0.673927124 0.386 0.715 0.388 ENR+CD-2 S100a11 Tm4sf41 0.672 0.695786283 0.344 0.568 0.228 ENR+CD-2 Tm4sf4 Clps9 0.67 0.28795985 0.34 0.826 0.46 ENR+CD-2 Clps D17H6S56E−55 0.668 0.577220844 0.336 0.687 0.402 ENR+CD-2 D17H6S56E−5 Guca2a7 0.666 0.436541828 0.332 0.733 0.394 ENR+CD-2 Guca2a Cd24a5 0.662 0.424451845 0.324 0.822 0.61 ENR+CD-2 Cd24a Tac14 0.66 0.51582336 0.32 0.492 0.167 ENR+CD-2 Tac1 Ifitm35 0.656 0.476562816 0.312 0.724 0.444 ENR+CD-2 Ifitm3 Cpe 0.653 0.768488569 0.306 0.42 0.107 ENR+CD-2 Cpe Scg2 0.65 0.909979206 0.3 0.381 0.077 ENR+CD-2 Scg2 Gm101046 0.65 0.486952231 0.3 0.536 0.208 ENR+CD-2 Gm10104 Cfi1 0.645 0.699855748 0.29 0.429 0.134 ENR+CD-2 Cfi Ctsl3 0.644 0.636553795 0.288 0.511 0.237 ENR+CD-2 Ctsl Cldn44 0.644 0.499420163 0.288 0.585 0.3 ENR+CD-2 Cldn4 Agr26 0.643 0.297331723 0.286 0.754 0.469 ENR+CD-2 Agr2 Gm15293 0.638 0.537476239 0.276 0.414 0.123 ENR+CD-2 Gm15293 Ghrl 0.634 0.271791802 0.268 0.421 0.14 ENR+CD-2 Ghrl Ly6e1 0.631 0.560375359 0.262 0.505 0.252 ENR+CD-2 Ly6e Cst31 0.629 0.434601539 0.258 0.687 0.461 ENR+CD-2 Cst3 Defa267 0.626 0.348255978 0.252 0.566 0.282 ENR+CD-2 Defa26 Defa-rs71 0.625 0.470261981 0.25 0.424 0.155 ENR+CD-2 Defa-rs7 Reg3g1 0.62 0.47864056 0.24 0.435 0.192 ENR+CD-2 Reg3g Rdh101 0.618 0.600965297 0.236 0.364 0.122 ENR+CD-2 Rdh10 Lect2 0.611 0.737151824 0.222 0.31 0.09 ENR+CD-2 Lect2 Gadd45g 0.61 0.53691856 0.22 0.376 0.158 ENR+CD-2 Gadd45g Wbp56 0.61 0.353807258 0.22 0.689 0.486 ENR+CD-2 Wbp5 Pcsk1 0.607 0.595290862 0.214 0.313 0.097 ENR+CD-2 Pcsk1 Lamp22 0.607 0.440830518 0.214 0.482 0.282 ENR+CD-2 Lamp2 Rnase42 0.607 0.417457058 0.214 0.548 0.347 ENR+CD-2 Rnase4 Serpinb1a 0.606 0.46729396 0.212 0.453 0.248 ENR+CD-2 Serpinb1a Cyp2c55 0.605 0.475836171 0.21 0.382 0.172 ENR+CD-2 Cyp2c55 Gm14850 0.605 0.333427165 0.21 0.385 0.153 ENR+CD-2 Gm14850 Nupr11 0.603 0.328483346 0.206 0.444 0.223 ENR+CD-2 Nupr1 Ttr 0.601 0.691722383 0.202 0.331 0.133 ENR+CD-2 Ttr Gm152847 0.911 1.417767489 0.822 1 0.677 ENR+CD-3 Gm15284 Defa38 0.91 1.48438864 0.82 0.989 0.357 ENR+CD-3 Defa3 Ang48 0.906 1.481959089 0.812 0.992 0.419 ENR+CD-3 Ang4 Itln18 0.902 1.30581211 0.804 1 0.732 ENR+CD-3 Itln1 Defa178 0.9 1.251411894 0.8 1 0.692 ENR+CD-3 Defa17 Lyz18 0.899 1.379689576 0.798 0.999 0.638 ENR+CD-3 Lyz1 Defa-rs18 0.893 1.30730474 0.786 0.988 0.397 ENR+CD-3 Defa-rs1 Defa246 0.892 1.162558349 0.784 1 0.887 ENR+CD-3 Defa24 Mmp79 0.882 1.300404782 0.764 0.983 0.469 ENR+CD-3 Mmp7 Defa218 0.868 1.402843208 0.736 0.932 0.306 ENR+CD-3 Defa21 Gm148519 0.862 1.309336088 0.724 0.95 0.403 ENR+CD-3 Gm14851 Defa228 0.846 1.328756325 0.692 0.885 0.278 ENR+CD-3 Defa22 Tff38 0.839 0.921100656 0.678 0.999 0.656 ENR+CD-3 Tff3 Gm153158 0.816 1.235877475 0.632 0.828 0.262 ENR+CD-3 Gm15315 AY7611858 0.808 1.152150262 0.616 0.834 0.297 ENR+CD-3 AY761185 Clps10 0.772 0.827134581 0.544 0.872 0.435 ENR+CD-3 Clps Chgb7 0.74 0.319575495 0.48 0.858 0.413 ENR+CD-3 Chgb Spink47 0.737 0.379668581 0.474 0.981 0.736 ENR+CD-3 Spink4 AY7611848 0.734 0.645499385 0.468 0.767 0.347 ENR+CD-3 AY761184 Guca2a8 0.727 0.812298742 0.454 0.763 0.374 ENR+CD-3 Guca2a Sct9 0.725 0.872798507 0.45 0.661 0.241 ENR+CD-3 Sct Agr27 0.71 0.725107239 0.42 0.765 0.454 ENR+CD-3 Agr2 Gm101047 0.708 0.952024661 0.416 0.582 0.186 ENR+CD-3 Gm10104 Mptx22 0.7 1.409945284 0.4 0.513 0.132 ENR+CD-3 Mptx2 Defa268 0.688 0.780710181 0.376 0.611 0.261 ENR+CD-3 Defa26 Ifitm16 0.683 0.758241776 0.366 0.593 0.255 ENR+CD-3 Ifitm1 Reg3b5 0.674 0.741838574 0.348 0.516 0.192 ENR+CD-3 Reg3b Defa-rs72 0.668 0.966768154 0.336 0.455 0.137 ENR+CD-3 Defa-rs7 S100a66 0.668 0.608871913 0.336 0.611 0.332 ENR+CD-3 S100a6 Gm152931 0.659 1.003467707 0.318 0.416 0.11 ENR+CD-3 Gm15293 Clu10 0.659 0.803118786 0.318 0.481 0.171 ENR+CD-3 Clu Gm148501 0.653 0.846884672 0.306 0.428 0.135 ENR+CD-3 Gm14850 Thbs16 0.653 0.752857526 0.306 0.503 0.227 ENR+CD-3 Thbs1 Cck5 0.65 0.394319127 0.3 0.51 0.23 ENR+CD-3 Cck Defa23 0.645 0.837081767 0.29 0.421 0.151 ENR+CD-3 Defa23 S100a117 0.64 0.561318422 0.28 0.597 0.394 ENR+CD-3 S100a11 Nupr12 0.638 0.82665142 0.276 0.451 0.212 ENR+CD-3 Nupr1 D17H6S56E−56 0.633 0.525823846 0.266 0.598 0.405 ENR+CD-3 D17H6S56E−5 Ifitm36 0.632 0.48982756 0.264 0.634 0.448 ENR+CD-3 Ifitm3 Gcg4 0.631 0.443385283 0.262 0.411 0.158 ENR+CD-3 Gcg Defa5 0.628 0.887931096 0.256 0.33 0.08 ENR+CD-3 Defa5 Fxyd36 0.627 0.59934023 0.254 0.554 0.369 ENR+CD-3 Fxyd3 Cd24a6 0.627 0.444065871 0.254 0.723 0.618 ENR+CD-3 Cd24a Gm152997 0.626 0.457038003 0.252 0.499 0.259 ENR+CD-3 Gm15299 Lyz2 0.621 0.810292369 0.242 0.339 0.108 ENR+CD-3 Lyz2 Reg3g2 0.618 0.752320317 0.236 0.395 0.189 ENR+CD-3 Reg3g Gm15292 0.613 0.781588719 0.226 0.323 0.109 ENR+CD-3 Gm15292 Cldn45 0.612 0.506487127 0.224 0.489 0.304 ENR+CD-3 Cldn4 Ghrl1 0.604 0.512540452 0.208 0.34 0.142 ENR+CD-3 Ghrl Defa247 0.978 1.653810125 0.956 1 0.9 ENR+CD-4 Defa24 Defa179 0.971 1.717509942 0.942 1 0.729 ENR+CD-4 Defa17 Defa-rs19 0.969 1.915928136 0.938 1 0.466 ENR+CD-4 Defa-rs1 Defa39 0.956 1.874812807 0.912 1 0.431 ENR+CD-4 Defa3 Gm152848 0.948 1.894058904 0.896 1 0.715 ENR+CD-4 Gm15284 AY7611859 0.944 1.735123513 0.888 0.986 0.354 ENR+CD-4 AY761185 Itln19 0.94 1.683069674 0.88 1 0.763 ENR+CD-4 Itln1 Ang49 0.926 1.830271754 0.852 0.991 0.487 ENR+CD-4 Ang4 Gm153159 0.915 1.86256915 0.83 0.963 0.324 ENR+CD-4 Gm15315 Lyz19 0.896 1.807121426 0.792 0.991 0.681 ENR+CD-4 Lyz1 Clps11 0.893 1.472626516 0.786 0.986 0.482 ENR+CD-4 Clps Defa219 0.892 1.733880333 0.784 0.981 0.378 ENR+CD-4 Defa21 Mmp710 0.889 1.332678006 0.778 0.995 0.529 ENR+CD-4 Mmp7 Gm1485110 0.888 1.893476735 0.776 0.991 0.466 ENR+CD-4 Gm14851 Tff39 0.884 1.269128067 0.768 1 0.696 ENR+CD-4 Tff3 Defa269 0.877 1.511985309 0.754 0.916 0.291 ENR+CD-4 Defa26 Defa-rs73 0.867 1.553365651 0.734 0.846 0.16 ENR+CD-4 Defa-rs7 Defa229 0.86 1.867440887 0.72 0.935 0.347 ENR+CD-4 Defa22 AY7611849 0.848 1.603050723 0.696 0.935 0.39 ENR+CD-4 AY761184 Gm152998 0.842 1.401888038 0.684 0.874 0.273 ENR+CD-4 Gm15299 Gm101048 0.839 1.636002805 0.678 0.808 0.224 ENR+CD-4 Gm10104 Guca2a9 0.829 1.263146743 0.658 0.907 0.414 ENR+CD-4 Guca2a Spink48 0.825 1.128028718 0.65 0.995 0.764 ENR+CD-4 Spink4 Defa231 0.819 1.298642496 0.638 0.78 0.169 ENR+CD-4 Defa23 Gm148502 0.807 1.586456887 0.614 0.729 0.159 ENR+CD-4 Gm14850 Gm152921 0.791 1.235848407 0.582 0.696 0.12 ENR+CD-4 Gm15292 Nupr13 0.776 1.42316347 0.552 0.71 0.23 ENR+CD-4 Nupr1 Gm152932 0.759 1.689396485 0.518 0.626 0.138 ENR+CD-4 Gm15293 Lyz21 0.753 1.312597791 0.506 0.617 0.125 ENR+CD-4 Lyz2 Agr28 0.746 0.904952546 0.492 0.846 0.488 ENR+CD-4 Agr2 Defa51 0.739 1.427966915 0.478 0.565 0.1 ENR+CD-4 Defa5 Gm9765 0.689 1.049917065 0.378 0.453 0.077 ENR+CD-4 Gm9765 Ang2 0.685 1.029087335 0.37 0.439 0.068 ENR+CD-4 Ang2 Gm6696 0.685 0.932998515 0.37 0.444 0.073 ENR+CD-4 Gm6696 Pnliprp2 0.683 1.090192172 0.366 0.463 0.106 ENR+CD-4 Pnliprp2 Gm7861 0.682 0.857146045 0.364 0.444 0.073 ENR+CD-4 Gm7861 Defa25 0.667 0.916936303 0.334 0.388 0.051 ENR+CD-4 Defa25 Guca2b1 0.665 0.784158582 0.33 0.477 0.146 ENR+CD-4 Guca2b Rnase1 0.644 0.872333667 0.288 0.421 0.135 ENR+CD-4 Rnase1 Rnase43 0.644 0.517518187 0.288 0.626 0.36 ENR+CD-4 Rnase4 Gm21498 0.643 0.85822942 0.286 0.341 0.053 ENR+CD-4 Gm21498 Ang6 0.641 0.855478261 0.282 0.341 0.059 ENR+CD-4 Ang6 Cd24a7 0.639 0.379091879 0.278 0.804 0.627 ENR+CD-4 Cd24a Ssr41 0.624 0.402782071 0.248 0.724 0.576 ENR+CD-4 Ssr4 Selm2 0.622 0.541045922 0.244 0.486 0.249 ENR+CD-4 Selm Ang5 0.619 0.749613346 0.238 0.294 0.054 ENR+CD-4 Ang5 Cd632 0.618 0.368937721 0.236 0.715 0.512 ENR+CD-4 Cd63 Tmed6 0.617 0.492982028 0.234 0.5 0.278 ENR+CD-4 Tmed6 Ang 0.616 0.593728014 0.232 0.36 0.128 ENR+CD-4 Ang Serp1 0.616 0.437250688 0.232 0.565 0.352 ENR+CD-4 Serp1 Mptx23 0.614 1.332002551 0.228 0.397 0.181 ENR+CD-4 Mptx2 Muc2 0.607 0.701039035 0.214 0.276 0.061 ENR+CD-4 Muc2 Habp2 0.606 0.5665122 0.212 0.276 0.06 ENR+CD-4 Habp2 Vimp 0.605 0.607806321 0.21 0.364 0.164 ENR+CD-4 Vimp Sec11c 0.605 0.390461867 0.21 0.542 0.345 ENR+CD-4 Sec11c P4hb1 0.603 0.267765547 0.206 0.762 0.591 ENR+CD-4 P4hb Fcgbp5 0.601 0.420617741 0.202 0.439 0.231 ENR+CD-4 Fcgbp Muc13 0.601 0.408921351 0.202 0.491 0.289 ENR+CD-4 Muc13 Cpe1 0.868 2.061769681 0.736 0.801 0.126 Neuro-1 Cpe Chgb8 0.861 2.411534834 0.722 0.875 0.47 Neuro-1 Chgb Chga5 0.858 1.923833184 0.716 0.838 0.216 Neuro-1 Chga Neurod1 0.856 1.900034487 0.712 0.757 0.058 Neuro-1 Neurod1 Serpinb1a1 0.825 1.52674678 0.65 0.809 0.259 Neuro-1 Serpinb1a Tm4sf42 0.813 1.359021605 0.626 0.801 0.253 Neuro-1 Tm4sf4 Pcsk11 0.81 1.645003246 0.62 0.706 0.108 Neuro-1 Pcsk1 Sepp1 0.799 1.370027544 0.598 0.728 0.162 Neuro-1 Sepp1 Hepacam2 0.781 1.464877563 0.562 0.632 0.077 Neuro-1 Hepacam2 Hmgn3 0.78 1.564671978 0.56 0.61 0.052 Neuro-1 Hmgn3 Ptprn2 0.776 1.330115601 0.552 0.61 0.059 Neuro-1 Ptprn2 Scg5 0.765 1.399166134 0.53 0.574 0.043 Neuro-1 Scg5 Fam183b 0.765 1.373925491 0.53 0.588 0.061 Neuro-1 Fam183b Sct10 0.754 1.905545228 0.508 0.728 0.294 Neuro-1 Sct Scg21 0.747 2.097630337 0.494 0.566 0.1 Neuro-1 Scg2 Rnf321 0.739 1.31568039 0.478 0.618 0.187 Neuro-1 Rnf32 Ddc 0.736 1.096785677 0.472 0.566 0.098 Neuro-1 Ddc Prnp 0.724 1.19680042 0.448 0.493 0.044 Neuro-1 Prnp Tuba1a4 0.723 0.975817209 0.446 0.632 0.213 Neuro-1 Tuba1a Sult1d11 0.722 1.059273546 0.444 0.574 0.138 Neuro-1 Sult1d1 Fxyd37 0.721 0.89196613 0.442 0.757 0.388 Neuro-1 Fxyd3 Cyp4b1 0.719 1.232809916 0.438 0.5 0.071 Neuro-1 Cyp4b1 Cystm12 0.714 0.63886326 0.428 0.86 0.638 Neuro-1 Cystm1 Rab3c 0.713 1.158868725 0.426 0.463 0.034 Neuro-1 Rab3c Lect21 0.712 1.534495074 0.424 0.515 0.105 Neuro-1 Lect2 Scgn 0.712 1.443239579 0.424 0.456 0.033 Neuro-1 Scgn 5330417C22Rik 0.711 0.96024513 0.422 0.522 0.097 Neuro-1 5330417C22Rik Resp18 0.71 1.339151365 0.42 0.478 0.06 Neuro-1 Resp18 Cnot6l 0.708 0.994980747 0.416 0.515 0.097 Neuro-1 Cnot6l Pcsk1n 0.707 1.262864306 0.414 0.449 0.036 Neuro-1 Pcsk1n Ddx51 0.707 0.52010653 0.414 0.89 0.642 Neuro-1 Ddx5 Prkar1a 0.706 0.794888222 0.412 0.647 0.254 Neuro-1 Prkar1a Hopx2 0.705 0.812314443 0.41 0.684 0.313 Neuro-1 Hopx Itm2c 0.704 0.907713892 0.408 0.581 0.178 Neuro-1 Itm2c Map1b 0.703 1.071367345 0.406 0.456 0.046 Neuro-1 Map1b Btg21 0.702 0.819592839 0.404 0.618 0.232 Neuro-1 Btg2 Cplx2 0.701 0.992904519 0.402 0.463 0.058 Neuro-1 Cplx2 Muc131 0.701 0.722582624 0.402 0.669 0.287 Neuro-1 Muc13 Cst32 0.698 0.765923639 0.396 0.765 0.48 Neuro-1 Cst3 Krt20 0.697 1.472795372 0.394 0.456 0.074 Neuro-1 Krt20 Slc18a1 0.696 0.99031306 0.392 0.441 0.044 Neuro-1 Slc18a1 Maged1 0.696 0.796949416 0.392 0.566 0.173 Neuro-1 Maged1 Gm609 0.693 0.847865386 0.386 0.449 0.056 Neuro-1 Gm609 Olfm1 0.692 0.984734604 0.384 0.412 0.024 Neuro-1 Olfm1 Gadd45g1 0.691 1.060556065 0.382 0.537 0.174 Neuro-1 Gadd45g Dpp4 0.69 1.078563799 0.38 0.478 0.109 Neuro-1 Dpp4 Arf51 0.689 0.694678628 0.378 0.632 0.267 Neuro-1 Arf5 Sis1 0.687 0.945039382 0.374 0.559 0.206 Neuro-1 Sis Cacna2d1 0.686 1.046893483 0.372 0.397 0.024 Neuro-1 Cacna2d1 Slc25a44 0.684 0.698704815 0.368 0.662 0.317 Neuro-1 Slc25a4 Ceacam10 0.683 1.237660611 0.366 0.404 0.039 Neuro-1 Ceacam10 Peg3 0.683 1.165933368 0.366 0.434 0.068 Neuro-1 Peg3 Bex2 0.683 0.99870905 0.366 0.426 0.06 Neuro-1 Bex2 Hk2 0.681 0.828213419 0.362 0.493 0.129 Neuro-1 Hk2 Gng12 0.681 0.715728427 0.362 0.529 0.159 Neuro-1 Gng12 Cd813 0.68 0.624985987 0.36 0.772 0.488 Neuro-1 Cd81 Pam 0.679 1.058682168 0.358 0.419 0.064 Neuro-1 Pam Akap9 0.679 0.641135065 0.358 0.669 0.312 Neuro-1 Akap9 Syt13 0.678 0.969957383 0.356 0.382 0.025 Neuro-1 Syt13 Selm3 0.678 0.729440399 0.356 0.588 0.25 Neuro-1 Selm Rfx6 0.677 1.118582385 0.354 0.382 0.027 Neuro-1 Rfx6 Aplp1 0.677 0.985362262 0.354 0.39 0.035 Neuro-1 Aplp1 Txnip1 0.677 0.710016729 0.354 0.684 0.355 Neuro-1 Txnip Ubl3 0.676 0.729918323 0.352 0.493 0.133 Neuro-1 Ubl3 Selk 0.676 0.660090551 0.352 0.588 0.248 Neuro-1 Selk Igfbp2 0.674 1.640894044 0.348 0.419 0.076 Neuro-1 Igfbp2 Gch1 0.674 0.839133061 0.348 0.419 0.067 Neuro-1 Gch1 Wbp57 0.674 0.513228435 0.348 0.794 0.502 Neuro-1 Wbp5 Tpm4 0.673 0.674267156 0.346 0.603 0.268 Neuro-1 Tpm4 Mien1 0.673 0.64287874 0.346 0.544 0.195 Neuro-1 Mien1 Tax1bp14 0.672 0.588102013 0.344 0.757 0.467 Neuro-1 Tax1bp1 Scg3 0.669 0.993218753 0.338 0.36 0.021 Neuro-1 Scg3 Spcs21 0.669 0.521967801 0.338 0.721 0.38 Neuro-1 Spcs2 Pla2g2f 0.667 0.991923013 0.334 0.382 0.046 Neuro-1 Pla2g2f Phldb2 0.666 0.795150054 0.332 0.419 0.083 Neuro-1 Phldb2 Calm16 0.666 0.346774953 0.332 0.926 0.875 Neuro-1 Calm1 Ttr1 0.665 1.085323621 0.33 0.463 0.148 Neuro-1 Ttr Runx1t1 0.664 1.105954969 0.328 0.346 0.017 Neuro-1 Runx1t1 Cxxc5 0.664 0.847365801 0.328 0.397 0.068 Neuro-1 Cxxc5 Lgals3bp 0.663 0.801567078 0.326 0.485 0.166 Neuro-1 Lgals3bp Ngfrap12 0.663 0.673121868 0.326 0.522 0.205 Neuro-1 Ngfrap1 Cd633 0.663 0.5234039 0.326 0.772 0.513 Neuro-1 Cd63 Tac15 0.662 2.258223311 0.324 0.478 0.197 Neuro-1 Tac1 Insm1 0.662 1.015476886 0.324 0.346 0.02 Neuro-1 Insm1 Oaz14 0.662 0.401184211 0.324 0.89 0.62 Neuro-1 Oaz1 Gm15200 0.661 1.021694868 0.322 0.368 0.045 Neuro-1 Gm15200 Marcks 0.66 0.659513021 0.32 0.559 0.243 Neuro-1 Marcks St18 0.659 0.973607463 0.318 0.338 0.02 Neuro-1 St18 Camk2n1 0.658 0.802513074 0.316 0.412 0.098 Neuro-1 Camk2n1 Fgd2 0.657 0.842573313 0.314 0.338 0.022 Neuro-1 Fgd2 Scp2 0.657 0.600343936 0.314 0.551 0.232 Neuro-1 Scp2 Ddx6 0.657 0.584958973 0.314 0.588 0.274 Neuro-1 Ddx6 Nkx2-2 0.656 0.954889416 0.312 0.338 0.026 Neuro-1 Nkx2-2 Cacna1a 0.654 0.777140018 0.308 0.346 0.034 Neuro-1 Cacna1a Etv1 0.653 1.00755855 0.306 0.324 0.017 Neuro-1 Etv1 Cpq 0.653 0.798825882 0.306 0.375 0.066 Neuro-1 Cpq Tusc3 0.652 0.815489525 0.304 0.39 0.085 Neuro-1 Tusc3 Ets1 0.652 0.811009911 0.304 0.331 0.023 Neuro-1 Ets1 Btg12 0.652 0.69571158 0.304 0.463 0.159 Neuro-1 Btg1 Rph3al 0.651 0.922069171 0.302 0.338 0.036 Neuro-1 Rph3al Mtch1 0.651 0.695188098 0.302 0.456 0.152 Neuro-1 Mtch1 Plac82 0.651 0.688093339 0.302 0.735 0.59 Neuro-1 Plac8 Prdx5 0.65 0.660838495 0.3 0.485 0.183 Neuro-1 Prdx5 D4Wsu53e 0.65 0.452838143 0.3 0.684 0.371 Neuro-1 D4Wsu53e Nenf 0.649 0.744694602 0.298 0.404 0.108 Neuro-1 Nenf Ccnl1 0.648 0.484337397 0.296 0.588 0.274 Neuro-1 Ccnl1 Ubb4 0.648 0.322781792 0.296 0.875 0.741 Neuro-1 Ubb Rhob 0.647 0.74053023 0.294 0.382 0.087 Neuro-1 Rhob Atp6v1b2 0.647 0.738016702 0.294 0.397 0.101 Neuro-1 Atp6v1b2 Eid1 0.646 0.673275145 0.292 0.39 0.092 Neuro-1 Eid1 Rap1a 0.644 0.623024799 0.288 0.456 0.167 Neuro-1 Rap1a Gabarapl2 0.643 0.559841146 0.286 0.434 0.14 Neuro-1 Gabarapl2 Clk1 0.643 0.485673461 0.286 0.5 0.196 Neuro-1 Clk1 Calm21 0.643 0.408325971 0.286 0.794 0.582 Neuro-1 Calm2 Gadd45a 0.642 1.076853509 0.284 0.368 0.088 Neuro-1 Gadd45a Ncald 0.642 0.794960574 0.284 0.346 0.061 Neuro-1 Ncald Lcorl 0.642 0.786403022 0.284 0.382 0.095 Neuro-1 Lcorl Phip 0.642 0.627728651 0.284 0.434 0.147 Neuro-1 Phip Acly 0.642 0.545261691 0.284 0.5 0.213 Neuro-1 Acly Nisch 0.641 0.650495823 0.282 0.463 0.184 Neuro-1 Nisch Gcc2 0.641 0.635252151 0.282 0.515 0.237 Neuro-1 Gcc2 Hsbp11 0.641 0.503687612 0.282 0.588 0.311 Neuro-1 Hsbp1 Ostc1 0.641 0.469101583 0.282 0.625 0.346 Neuro-1 Ostc Laptm4a 0.641 0.466806511 0.282 0.618 0.366 Neuro-1 Laptm4a Hsp90b12 0.641 0.356420902 0.282 0.868 0.71 Neuro-1 Hsp90b1 Celf3 0.64 0.703373457 0.28 0.301 0.018 Neuro-1 Celf3 Atp2b1 0.64 0.549518999 0.28 0.507 0.216 Neuro-1 Atp2b1 H3f3a2 0.64 0.403909324 0.28 0.757 0.473 Neuro-1 H3f3a Wnt3 0.639 0.828878937 0.278 0.316 0.039 Neuro-1 Wnt3 Ift20 0.639 0.623180713 0.278 0.434 0.157 Neuro-1 Ift20 H2-D12 0.639 0.508253815 0.278 0.647 0.372 Neuro-1 H2-D1 Gfra3 0.638 1.117930727 0.276 0.294 0.018 Neuro-1 Gfra3 Rap1b 0.638 0.754104706 0.276 0.382 0.112 Neuro-1 Rap1b Afg3l2 0.638 0.685814481 0.276 0.412 0.136 Neuro-1 Afg3l2 Mrfap1 0.638 0.44059393 0.276 0.61 0.324 Neuro-1 Mrfap1 Tmem59 0.637 0.50045587 0.274 0.566 0.294 Neuro-1 Tmem59 Gnai2 0.637 0.493258098 0.274 0.478 0.188 Neuro-1 Gnai2 Ndufa14 0.637 0.450731142 0.274 0.669 0.376 Neuro-1 Ndufa1 Serinc1 0.636 0.582311398 0.272 0.397 0.117 Neuro-1 Serinc1 Sh3bgrl 0.635 0.515924035 0.27 0.426 0.147 Neuro-1 Sh3bgrl Ssr2 0.635 0.386689782 0.27 0.728 0.463 Neuro-1 Ssr2 Tspan12 0.634 0.619319573 0.268 0.397 0.129 Neuro-1 Tspan12 Clcn3 0.634 0.581409636 0.268 0.449 0.179 Neuro-1 Clcn3 Morf4l2 0.634 0.535528125 0.268 0.441 0.164 Neuro-1 Morf4l2 Bsg6 0.634 0.303402495 0.268 0.941 0.731 Neuro-1 Bsg Fev 0.632 0.86765879 0.264 0.287 0.022 Neuro-1 Fev Bambi 0.632 0.741238669 0.264 0.309 0.043 Neuro-1 Bambi Slc35g2 0.632 0.733617229 0.264 0.294 0.029 Neuro-1 Slc35g2 Ece1 0.632 0.721062527 0.264 0.338 0.075 Neuro-1 Ece1 Tle1 0.632 0.706991013 0.264 0.353 0.09 Neuro-1 Tle1 Cdkn1b1 0.632 0.658281295 0.264 0.419 0.157 Neuro-1 Cdkn1b Impa12 0.632 0.502041566 0.264 0.449 0.175 Neuro-1 Impa1 B2m 0.632 0.442503547 0.264 0.706 0.428 Neuro-1 B2m Krt71 0.632 0.39352623 0.264 0.618 0.335 Neuro-1 Krt7 Sec61b3 0.632 0.33541501 0.264 0.801 0.594 Neuro-1 Sec61b Dpysl22 0.631 0.603572304 0.262 0.382 0.12 Neuro-1 Dpysl2 Surf4 0.631 0.528835041 0.262 0.449 0.185 Neuro-1 Surf4 Ctsl4 0.631 0.439165318 0.262 0.537 0.261 Neuro-1 Ctsl Neurog3 0.63 1.862919081 0.26 0.301 0.049 Neuro-1 Neurog3 Vwa5b2 0.63 0.731717519 0.26 0.287 0.025 Neuro-1 Vwa5b2 Jhdm1d 0.63 0.645037441 0.26 0.316 0.053 Neuro-1 Jhdm1d Tspan13 0.63 0.583500389 0.26 0.471 0.21 Neuro-1 Tspan13 Calm32 0.63 0.522874254 0.26 0.551 0.31 Neuro-1 Calm3 Gnb22 0.63 0.509441786 0.26 0.61 0.351 Neuro-1 Gnb2 Baiap2l2 0.629 0.584108533 0.258 0.397 0.135 Neuro-1 Baiap2l2 Kdelr2 0.629 0.466308675 0.258 0.566 0.308 Neuro-1 Kdelr2 Arpc51 0.628 0.431600143 0.256 0.581 0.324 Neuro-1 Arpc5 Eif5 0.628 0.331048493 0.256 0.757 0.506 Neuro-1 Eif5 Gpr112 0.627 0.767151791 0.254 0.272 0.017 Neuro-1 Gpr112 Atg3 0.627 0.509100865 0.254 0.382 0.119 Neuro-1 Atg3 Nudt4 0.627 0.508601246 0.254 0.39 0.129 Neuro-1 Nudt4 Atp6v0b1 0.627 0.500063354 0.254 0.478 0.216 Neuro-1 Atp6v0b Rev3l 0.627 0.499944614 0.254 0.382 0.118 Neuro-1 Rev3l Nbea 0.626 0.693383632 0.252 0.316 0.061 Neuro-1 Nbea Gclm 0.626 0.47904226 0.252 0.419 0.157 Neuro-1 Gclm Rab11a 0.626 0.464935682 0.252 0.478 0.217 Neuro-1 Rab11a Cd164 0.626 0.45439964 0.252 0.434 0.166 Neuro-1 Cd164 Uqcc2 0.626 0.364120338 0.252 0.654 0.39 Neuro-1 Uqcc2 Pkdcc 0.625 0.582903333 0.25 0.316 0.062 Neuro-1 Pkdcc Rnf128 0.625 0.365771523 0.25 0.588 0.322 Neuro-1 Rnf128 Hmgcr 0.624 0.519532934 0.248 0.434 0.181 Neuro-1 Hmgcr Ube2b 0.624 0.434372908 0.248 0.522 0.266 Neuro-1 Ube2b Itm2b1 0.624 0.352418292 0.248 0.699 0.46 Neuro-1 Itm2b Atp6v0d1 0.623 0.501170413 0.246 0.324 0.071 Neuro-1 Atp6v0d1 Sdcbp 0.623 0.44728396 0.246 0.522 0.275 Neuro-1 Sdcbp Snap25 0.622 0.733085499 0.244 0.265 0.019 Neuro-1 Snap25 Gnptg 0.622 0.684923176 0.244 0.309 0.065 Neuro-1 Gnptg Jak1 0.622 0.529762102 0.244 0.397 0.15 Neuro-1 Jak1 Tmed3 0.622 0.507178669 0.244 0.404 0.152 Neuro-1 Tmed3 Tmem176b 0.622 0.448540008 0.244 0.522 0.272 Neuro-1 Tmem176b Pdap14 0.622 0.375444576 0.244 0.669 0.41 Neuro-1 Pdap1 Htatsf1 0.621 0.641582192 0.242 0.382 0.145 Neuro-1 Htatsf1 Etnk1 0.621 0.57604006 0.242 0.331 0.085 Neuro-1 Etnk1 Msi2 0.621 0.55577455 0.242 0.397 0.151 Neuro-1 Msi2 Rab3d1 0.621 0.517415086 0.242 0.382 0.134 Neuro-1 Rab3d Atp6v1g1 0.621 0.440226679 0.242 0.5 0.255 Neuro-1 Atp6v1g1 Fkbp1a 0.621 0.434229581 0.242 0.537 0.267 Neuro-1 Fkbp1a Ccnl2 0.62 0.578906158 0.24 0.441 0.197 Neuro-1 Ccnl2 Fam135a 0.62 0.556454682 0.24 0.353 0.109 Neuro-1 Fam135a Prox11 0.62 0.537224344 0.24 0.368 0.121 Neuro-1 Prox1 Pdia32 0.62 0.385565878 0.24 0.765 0.585 Neuro-1 Pdia3 Tspan33 0.62 0.361026313 0.24 0.537 0.269 Neuro-1 Tspan3 Arf11 0.62 0.344187048 0.24 0.588 0.342 Neuro-1 Arf1 Cdhr5 0.619 0.588085284 0.238 0.353 0.11 Neuro-1 Cdhr5 Dgkd 0.619 0.584670256 0.238 0.346 0.104 Neuro-1 Dgkd Arl32 0.619 0.554441733 0.238 0.368 0.125 Neuro-1 Arl3 Tecpr1 0.619 0.544698414 0.238 0.316 0.075 Neuro-1 Tecpr1 Neb 0.618 1.171075878 0.236 0.301 0.072 Neuro-1 Neb Pafah1b1 0.618 0.443726027 0.236 0.463 0.224 Neuro-1 Pafah1b1 Dad11 0.618 0.389491382 0.236 0.588 0.342 Neuro-1 Dad1 Sqstm1 0.617 0.502684131 0.234 0.368 0.126 Neuro-1 Sqstm1 Npdc1 0.617 0.502104728 0.234 0.346 0.106 Neuro-1 Npdc1 Grcc10 0.617 0.458144986 0.234 0.485 0.252 Neuro-1 Grcc10 Atp6v0e 0.617 0.338596142 0.234 0.566 0.307 Neuro-1 Atp6v0e Gripap1 0.616 0.607988443 0.232 0.287 0.052 Neuro-1 Gripap1 Selt 0.616 0.500239096 0.232 0.419 0.177 Neuro-1 Selt Myo6 0.616 0.481571742 0.232 0.493 0.25 Neuro-1 Myo6 Ddost2 0.615 0.397225476 0.23 0.544 0.313 Neuro-1 Ddost Tcf25 0.615 0.361746655 0.23 0.507 0.261 Neuro-1 Tcf25 Ica1 0.614 0.495387984 0.228 0.301 0.068 Neuro-1 Ica1 Cyb5r31 0.614 0.478034094 0.228 0.397 0.165 Neuro-1 Cyb5r3 Egr14 0.614 0.37889108 0.228 0.64 0.404 Neuro-1 Egr1 Ankib1 0.613 0.607072595 0.226 0.287 0.059 Neuro-1 Ankib1 Pim2 0.613 0.584781157 0.226 0.243 0.016 Neuro-1 Pim2 D19Ertd737e 0.613 0.577184167 0.226 0.309 0.08 Neuro-1 D19Ertd737e Anapc5 0.613 0.326902542 0.226 0.485 0.238 Neuro-1 Anapc5 Nktr 0.612 0.451196678 0.224 0.39 0.16 Neuro-1 Nktr Adh11 0.611 0.707180854 0.222 0.404 0.194 Neuro-1 Adh1 Stxbp5l 0.611 0.683170041 0.222 0.243 0.019 Neuro-1 Stxbp5l Rimbp2 0.611 0.671794311 0.222 0.235 0.013 Neuro-1 Rimbp2 Ccdc104 0.611 0.566216037 0.222 0.331 0.106 Neuro-1 Ccdc104 Tmem661 0.611 0.520722237 0.222 0.353 0.126 Neuro-1 Tmem66 Os9 0.611 0.475052482 0.222 0.426 0.2 Neuro-1 Os9 Kif1b 0.611 0.412591612 0.222 0.346 0.115 Neuro-1 Kif1b Atrx 0.611 0.3500952 0.222 0.61 0.372 Neuro-1 Atrx Tpst2 0.61 0.611888595 0.22 0.265 0.046 Neuro-1 Tpst2 Grtp1 0.61 0.604200286 0.22 0.324 0.103 Neuro-1 Grtp1 Srrm21 0.61 0.372966321 0.22 0.713 0.47 Neuro-1 Srrm2 Srsf5 0.61 0.349263651 0.22 0.566 0.352 Neuro-1 Srsf5 Smpd3 0.609 0.618968949 0.218 0.324 0.106 Neuro-1 Smpd3 Pbx1 0.609 0.511977577 0.218 0.316 0.094 Neuro-1 Pbx1 Baz2b 0.609 0.505153383 0.218 0.346 0.121 Neuro-1 Baz2b Dnajc10 0.609 0.498149156 0.218 0.375 0.153 Neuro-1 Dnajc10 Plscr1 0.609 0.493688786 0.218 0.346 0.124 Neuro-1 Plscr1 Papss1 0.609 0.47358298 0.218 0.331 0.104 Neuro-1 Papss1 Sfr12 0.609 0.442694651 0.218 0.426 0.2 Neuro-1 Sfr1 2700089E24Rik 0.609 0.430347554 0.218 0.419 0.19 Neuro-1 2700089E24Rik Tmem208 0.609 0.345730582 0.218 0.471 0.235 Neuro-1 Tmem208 Cdkn1c 0.608 0.718787305 0.216 0.301 0.083 Neuro-1 Cdkn1c Ids 0.608 0.57633085 0.216 0.243 0.024 Neuro-1 Ids Ginm1 0.608 0.557913003 0.216 0.316 0.095 Neuro-1 Ginm1 Fndc3a 0.608 0.511356955 0.216 0.324 0.102 Neuro-1 Fndc3a Srp72 0.608 0.390566606 0.216 0.456 0.23 Neuro-1 Srp72 Sdf4 0.608 0.371109666 0.216 0.426 0.198 Neuro-1 Sdf4 Matr3 0.608 0.340711896 0.216 0.574 0.346 Neuro-1 Matr3 Tpd521 0.608 0.310807678 0.216 0.654 0.428 Neuro-1 Tpd52 Smim7 0.608 0.308843585 0.216 0.412 0.176 Neuro-1 Smim7 Rab15 0.607 0.52109546 0.214 0.272 0.056 Neuro-1 Rab15 Itfg1 0.607 0.51736313 0.214 0.316 0.101 Neuro-1 Itfg1 Srp14 0.607 0.310416224 0.214 0.515 0.278 Neuro-1 Srp14 Atf2 0.606 0.64125587 0.212 0.309 0.1 Neuro-1 Atf2 Zbtb20 0.606 0.629224674 0.212 0.257 0.044 Neuro-1 Zbtb20 Itpr1 0.606 0.593141036 0.212 0.257 0.043 Neuro-1 Itpr1 Akap8l 0.606 0.571486426 0.212 0.301 0.087 Neuro-1 Akap8l Kit 0.606 0.535581262 0.212 0.272 0.056 Neuro-1 Kit Eif4g3 0.606 0.392281288 0.212 0.324 0.102 Neuro-1 Eif4g3 Lrp11 0.605 0.470836804 0.21 0.235 0.024 Neuro-1 Lrp11 Slc38a11 0.605 0.397030605 0.21 0.397 0.175 Neuro-1 Slc38a1 Tmbim6 0.605 0.361225177 0.21 0.699 0.47 Neuro-1 Tmbim6 Ufm1 0.605 0.31958869 0.21 0.404 0.175 Neuro-1 Ufm1 Pfdn51 0.605 0.315328234 0.21 0.647 0.445 Neuro-1 Pfdn5 Nefm 0.604 1.056664137 0.208 0.221 0.013 Neuro-1 Nefm Cldn46 0.604 0.404174506 0.208 0.544 0.327 Neuro-1 Cldn4 Ywhab2 0.604 0.326678778 0.208 0.566 0.331 Neuro-1 Ywhab Ssr42 0.604 0.317084171 0.208 0.728 0.578 Neuro-1 Ssr4 Fryl 0.603 0.497185124 0.206 0.309 0.098 Neuro-1 Fryl Phyh 0.603 0.45174218 0.206 0.324 0.111 Neuro-1 Phyh Fam46a 0.603 0.444230155 0.206 0.309 0.097 Neuro-1 Fam46a Spcs11 0.603 0.432019153 0.206 0.559 0.35 Neuro-1 Spcs1 Kdm1a 0.603 0.421265714 0.206 0.324 0.112 Neuro-1 Kdm1a Atp8b1 0.603 0.408418464 0.206 0.485 0.274 Neuro-1 Atp8b1 Lamp23 0.603 0.373270994 0.206 0.507 0.3 Neuro-1 Lamp2 Kmt2e 0.603 0.367686215 0.206 0.404 0.186 Neuro-1 Kmt2e Rock1 0.603 0.337299181 0.206 0.434 0.214 Neuro-1 Rock1 Cryba2 0.602 0.722200536 0.204 0.221 0.016 Neuro-1 Cryba2 Klhl7 0.602 0.574774143 0.204 0.235 0.03 Neuro-1 Klhl7 Syp 0.602 0.550937539 0.204 0.213 0.008 Neuro-1 Syp Zmynd11 0.602 0.423387169 0.204 0.346 0.134 Neuro-1 Zmynd11 Ypel3 0.601 0.604612464 0.202 0.235 0.033 Neuro-1 Ypel3 Smim6 0.601 0.585922342 0.202 0.279 0.073 Neuro-1 Smim6 Cdhr2 0.601 0.524211462 0.202 0.294 0.088 Neuro-1 Cdhr2 Zfr 0.601 0.485674276 0.202 0.36 0.156 Neuro-1 Zfr Fyttd12 0.601 0.400754958 0.202 0.382 0.173 Neuro-1 Fyttd1 Tulp4 0.601 0.384054255 0.202 0.287 0.078 Neuro-1 Tulp4 Gfpt1 0.601 0.343263635 0.202 0.404 0.191 Neuro-1 Gfpt1 Chgb9 0.917 2.327697706 0.834 0.989 0.472 Neuro-2 Chgb Chga6 0.845 2.411948819 0.69 0.818 0.222 Neuro-2 Chga Reg45 0.834 3.086108186 0.668 0.818 0.388 Neuro-2 Reg4 Tac16 0.821 2.102281041 0.642 0.761 0.195 Neuro-2 Tac1 Afp 0.795 3.705224015 0.59 0.602 0.022 Neuro-2 Afp Tph1 0.769 2.033817286 0.538 0.557 0.025 Neuro-2 Tph1 Sepp11 0.76 1.6489138 0.52 0.636 0.168 Neuro-2 Sepp1 Gstt1 0.708 1.648193654 0.416 0.466 0.072 Neuro-2 Gstt1 S100a1 0.703 1.684653184 0.406 0.455 0.066 Neuro-2 S100a1 Ldha12 0.701 0.544641379 0.402 0.932 0.691 Neuro-2 Ldha Aldoa9 0.693 0.498704379 0.386 0.886 0.657 Neuro-2 Aldoa Me22 0.681 1.381349324 0.362 0.466 0.159 Neuro-2 Me2 Lgals411 0.681 0.425702026 0.362 0.932 0.804 Neuro-2 Lgals4 Cystm13 0.677 0.666414217 0.354 0.807 0.64 Neuro-2 Cystm1 Rab3c1 0.665 1.463902507 0.33 0.364 0.039 Neuro-2 Rab3c mt-Nd56 0.656 0.330158111 0.312 0.943 0.838 Neuro-2 mt-Nd5 Resp181 0.652 1.146002163 0.304 0.364 0.065 Neuro-2 Resp18 Ddc1 0.649 1.078479392 0.298 0.386 0.105 Neuro-2 Ddc Ucn3 0.64 1.539722718 0.28 0.284 0.005 Neuro-2 Ucn3 Tpbg 0.639 1.173945088 0.278 0.307 0.033 Neuro-2 Tpbg Pigr8 0.637 0.48784511 0.274 0.716 0.514 Neuro-2 Pigr Krt192 0.635 0.495719214 0.27 0.682 0.542 Neuro-2 Krt19 Pcsk12 0.632 1.159855021 0.264 0.364 0.118 Neuro-2 Pcsk1 Trpa1 0.63 1.170754886 0.26 0.261 0.002 Neuro-2 Trpa1 Rgs2 0.629 1.236480896 0.258 0.295 0.042 Neuro-2 Rgs2 Tm4sf5 0.629 0.722852056 0.258 0.477 0.26 Neuro-2 Tm4sf5 Phgr112 0.629 0.400915035 0.258 0.693 0.436 Neuro-2 Phgr1 Gng121 0.624 0.909339347 0.248 0.386 0.165 Neuro-2 Gng12 Akr1c14 0.622 1.252444111 0.244 0.273 0.033 Neuro-2 Akr1c14 Fam183b1 0.619 0.825344515 0.238 0.307 0.07 Neuro-2 Fam183b mt-Co15 0.619 0.253087133 0.238 0.989 0.919 Neuro-2 mt-Co1 Mt29 0.614 0.258638413 0.228 0.761 0.525 Neuro-2 Mt2 Gm51607 0.613 0.383107503 0.226 0.534 0.302 Neuro-2 Gm5160 Aldob5 0.612 0.33284222 0.224 0.636 0.452 Neuro-2 Aldob 2810025M15Rik 0.61 0.968354707 0.22 0.307 0.095 Neuro-2 2810025M15Rik Rasd1 0.608 0.95261514 0.216 0.261 0.05 Neuro-2 Rasd1 Glud1 0.608 0.79062616 0.216 0.409 0.233 Neuro-2 Glud1 Olfm410 0.606 0.461329406 0.212 0.511 0.297 Neuro-2 Olfm4 S100a13 0.605 1.010102518 0.21 0.25 0.045 Neuro-2 S100a13 Lmx1a 0.605 0.744675128 0.21 0.216 0.006 Neuro-2 Lmx1a Qdpr2 0.604 0.760405625 0.208 0.352 0.169 Neuro-2 Qdpr Vim3 0.603 0.860395063 0.206 0.307 0.114 Neuro-2 Vim Tm4sf204 0.603 0.479312866 0.206 0.568 0.418 Neuro-2 Tm4sf20 Table 1E. Results of ROC-test for Enteroendocrine-enriched marker genes from all in vivo isolated small intestinal epithelial cells (FIG. 5B EE InVivo) myAUC avg_diff power pct.1 pct.2 cluster gene Sct1 0.895 4.441579401 0.79 0.826 0.117 15 Sct Cpe 0.791 2.49298151 0.582 0.584 0.004 15 Cpe Neurod1 0.768 2.390970023 0.536 0.537 0.002 15 Neurod1 Chgb 0.747 4.217949736 0.494 0.5 0.009 15 Chgb Chga 0.733 3.19332977 0.466 0.495 0.044 15 Chga Pyy 0.724 3.902387734 0.448 0.458 0.015 15 Pyy Tm4sf410 0.704 1.072123268 0.408 0.621 0.258 15 Tm4sf4 Pcsk1 0.701 1.82008555 0.402 0.411 0.013 15 Pcsk1 Malat18 0.693 0.653493706 0.386 0.963 0.891 15 Malat1 Scg2 0.686 2.196639683 0.372 0.374 0.001 15 Scg2 Fam183b 0.678 1.696400795 0.356 0.363 0.008 15 Fam183b Cck 0.677 2.908997832 0.354 0.358 0.004 15 Cck Tuba1a1 0.674 1.338122488 0.348 0.363 0.016 15 Tuba1a Fxyd32 0.673 1.185527087 0.346 0.421 0.083 15 Fxyd3 Hepacam23 0.669 1.165044917 0.338 0.416 0.086 15 Hepacam2 Ddx56 0.661 0.623301847 0.322 0.716 0.565 15 Ddx5 Nts 0.652 4.938667765 0.304 0.337 0.047 15 Nts Insm1 0.652 1.238734111 0.304 0.305 0.001 15 Insm1 Ptprn22 0.651 1.404630386 0.302 0.316 0.017 15 Ptprn2 Krt77 0.65 1.323938982 0.3 0.416 0.146 15 Krt7 Cplx2 0.649 1.240295575 0.298 0.3 0.003 15 Cplx2 Scgn 0.647 1.540047379 0.294 0.295 0.001 15 Scgn Peg3 0.644 1.356044152 0.288 0.289 0.002 15 Peg3 Selm7 0.64 0.82025882 0.28 0.405 0.13 15 Selm Hopx7 0.638 0.926363644 0.276 0.389 0.135 15 Hopx Itm2c1 0.637 1.102633129 0.274 0.337 0.074 15 Itm2c Prnp 0.634 1.303812979 0.268 0.274 0.006 15 Prnp Car82 0.633 1.529182238 0.266 0.305 0.049 15 Car8 Pam 0.63 1.311657049 0.26 0.289 0.033 15 Pam Gch11 0.63 1.257519453 0.26 0.3 0.046 15 Gch1 Isl1 0.629 1.371287067 0.258 0.258 0.001 15 Isl1 Egr15 0.627 0.682695585 0.254 0.526 0.32 15 Egr1 Marcks4 0.626 0.940450751 0.252 0.347 0.111 15 Marcks Krt2011 0.626 0.523825991 0.252 0.779 0.664 15 Krt20 Maged1 0.624 1.065463701 0.248 0.268 0.022 15 Maged1 Rfx6 0.623 1.361875566 0.246 0.247 0.001 15 Rfx6 Resp18 0.621 1.452364039 0.242 0.242 0.001 15 Resp18 Cd817 0.62 0.872571881 0.24 0.4 0.195 15 Cd81 Ddc3 0.618 1.13237105 0.236 0.342 0.133 15 Ddc Ngfrap12 0.617 0.95111324 0.234 0.274 0.046 15 Ngfrap1 Hsp90ab19 0.617 0.31369222 0.234 0.842 0.726 15 Hsp90ab1 Pcsk1n 0.615 1.344770047 0.23 0.232 0.001 15 Pcsk1n Scg3 0.613 1.10155346 0.226 0.226 0 15 Scg3 Gfra3 0.613 1.009603294 0.226 0.226 0.001 15 Gfra3 Gm6093 0.613 0.875441764 0.226 0.258 0.034 15 Gm609 Wbp510 0.611 0.699030828 0.222 0.384 0.186 15 Wbp5 Cnot6l 0.608 0.880416395 0.216 0.258 0.046 15 Cnot6l 6-Jun 0.607 0.552274824 0.214 0.595 0.477 15 Jun Gcg 0.606 3.857236251 0.212 0.221 0.01 15 Gcg Vim 0.605 1.356353586 0.21 0.216 0.006 15 Vim Scg5 0.605 0.989739316 0.21 0.211 0 15 Scg5 Fos5 0.605 0.396425334 0.21 0.716 0.596 15 Fos Aplp12 0.603 1.084201386 0.206 0.237 0.035 15 Aplp1 5330417C22Rik3 0.603 0.83967063 0.206 0.263 0.062 15 5330417C22Rik Myl7 0.602 1.38794983 0.204 0.221 0.019 15 Myl7 Pax6 0.602 1.042831316 0.204 0.205 0.001 15 Pax6 Cldn42 0.601 0.704209507 0.202 0.274 0.071 15 Cldn4 KCTD121 0.6 0.823319344 0.2 0.226 0.024 15 KCTD12 Table 1F. InVivo Cluster 11 (Paneth Cells) vs Top 200 ENR + CD-4 cells (FIG. 5C InVivo vs ENR + CD4) Gene p_val avg_diff pct.1 pct.2 Fabp6 6.89E−73 2.794414465 0.799 0 Apoa1 1.28E−59 2.745285001 0.735 0.014 Fabp2 9.49E−71 2.729962201 0.942 0.13 Gm26924 4.31E−168 2.52809867 1 0.851 Gm15564 1.07E−77 2.437318135 0.878 0.038 Crip1 1.11E−65 2.201131282 0.894 0.096 Zg16 1.25E−28 2.162302471 0.471 0.019 Defa20 1.48E−44 2.046923898 0.635 0.024 Ccl6 1.34E−60 1.987268927 0.905 0.192 Olfm4 2.20E−31 1.74919956 0.434 0 Clec2h 8.09E−42 1.724494537 0.545 0 Defa26 3.78E−87 1.661421348 0.995 0.909 mmu-mir-6236 3.46E−46 1.656170899 0.587 0 Lars2 4.38E−53 1.62324169 0.91 0.409 Defa22 1.81E−90 1.597296473 1 0.923 AY761184 1.80E−67 1.551528962 1 0.923 Chd8 1.98E−14 1.547285814 0.36 0.072 Sepp1 2.99E−23 1.504693501 0.524 0.087 Spink3 1.31E−27 1.479284364 0.481 0.038 Defa2 1.06E−35 1.47360816 0.508 0.005 Gm1123 2.18E−39 1.425273122 0.73 0.106 Gm15292 3.66E−65 1.404298385 0.952 0.692 Gm21002 8.26E−32 1.403216059 0.466 0.005 Reg4 9.70E−39 1.364094895 0.899 0.548 Mptx1 1.12E−14 1.29579207 0.413 0.091 Pnliprp2 3.57E−33 1.252964435 0.878 0.442 Apoa4 3.00E−17 1.155744489 0.286 0.01 Sis 1.17E−16 1.154999476 0.439 0.072 Cps1 7.87E−20 1.134883345 0.344 0.019 Gm15308 3.15E−34 1.12386933 0.466 0 Lbh 1.19E−21 1.11711376 0.487 0.072 St3gal4 9.40E−18 1.095313054 0.317 0.019 Anpep 4.23E−22 1.09277501 0.524 0.087 Slc51a 6.69E−19 1.024249548 0.28 0 Mgam 1.27E−15 0.999087463 0.402 0.067 2200002D01Rik 2.83E−12 0.992108543 0.481 0.159 Ccl25 1.86E−17 0.989852511 0.354 0.034 Hpgd 1.40E−19 0.968811329 0.439 0.053 Mptx2 2.72E−13 0.949925415 0.788 0.423 Ces2e 6.56E−15 0.94678761 0.27 0.01 Pycard 7.85E−12 0.943278351 0.381 0.101 Krt20 2.76E−13 0.908829291 0.36 0.072 Bambi 2.02E−14 0.901391979 0.37 0.053 Ace2 8.63E−13 0.869654756 0.233 0.01 Sult1d1 5.02E−17 0.868941062 0.36 0.034 Clca3 6.45E−09 0.856399955 0.19 0.019 Pigr 2.86E−17 0.85359266 0.709 0.279 Gm10104 4.05E−24 0.834585815 0.979 0.798 Muc2 2.04E−16 0.832185644 0.661 0.245 Slc5a1 3.20E−15 0.829348878 0.36 0.043 Maoa 5.22E−13 0.820182098 0.302 0.034 Cdh17 1.55E−15 0.817891016 0.471 0.106 Otc 8.03E−13 0.799427168 0.228 0.01 Krt19 5.26E−12 0.797610341 0.63 0.293 Cyp4f14 2.15E−15 0.787921804 0.233 0 Plb1 1.64E−13 0.787790121 0.206 0 AI747448 3.14E−16 0.784452184 0.201 0.01 Slc6a19 5.96E−11 0.782890249 0.169 0 Atp5o 6.03E−10 0.748647472 0.508 0.202 Aoc1 8.16E−13 0.726366453 0.222 0.01 Sord 8.44E−11 0.723352746 0.365 0.082 Mep1b 4.62E−12 0.723175799 0.206 0.005 Prap1 1.25E−13 0.720704557 0.317 0.038 Mgst1 1.45E−12 0.717887883 0.481 0.144 Gm7849 4.94E−09 0.717557393 0.386 0.12 Enpep 2.11E−12 0.708946078 0.19 0 Atp1a1 7.56E−12 0.7036131 0.481 0.168 Cndp2 5.70E−10 0.699939528 0.238 0.024 Aldob 4.07E−09 0.698437585 0.423 0.139 Naaladl1 3.66E−11 0.694458684 0.212 0.014 Fos 5.76E−12 0.692995212 0.788 0.49 Muc3 4.89E−12 0.689025992 0.185 0 2210404O07Rik 2.49E−11 0.668864299 0.418 0.13 Dpep1 7.01E−10 0.666476273 0.153 0 Oat 5.12E−10 0.663503949 0.418 0.139 Reg3g 2.22E−10 0.662732291 0.608 0.274 Dgat1 1.81E−11 0.66075657 0.259 0.024 Pepd 1.35E−06 0.652370213 0.228 0.053 Uqcr10 3.69E−10 0.65050164 0.667 0.385 Tob1 1.02E−10 0.650029355 0.328 0.062 Cdx1 3.73E−07 0.645769015 0.354 0.144 Plcb3 3.17E−10 0.640070365 0.228 0.024 Lct 7.94E−09 0.639932045 0.138 0 Myo1a 6.34E−08 0.636556999 0.217 0.038 Pls1 1.26E−06 0.633128215 0.312 0.101 Slc27a4 2.37E−09 0.632437472 0.169 0.01 Guca2b 1.81E−12 0.626285536 0.804 0.476 Snord13 5.02E−09 0.621323384 0.402 0.125 Slc9a3r1 6.25E−07 0.619366422 0.27 0.072 Ckmt1 3.77E−09 0.614168327 0.296 0.067 Slc15a1 2.41E−07 0.610956158 0.143 0.005 Ggt1 2.36E−08 0.597187545 0.159 0.005 Apob 2.55E−06 0.59692589 0.206 0.062 Gfpt1 1.91E−08 0.590343443 0.434 0.197 Fbp2 6.63E−10 0.586392459 0.328 0.082 Sgk1 7.18E−12 0.584589889 0.238 0.014 Hpd 5.68E−09 0.58229397 0.265 0.043 Dpp4 4.71E−08 0.581900208 0.175 0.019 Klf4 5.30E−09 0.574982296 0.233 0.029 Hadha 4.09E−07 0.571458506 0.291 0.096 Cox5a 7.87E−08 0.563300928 0.503 0.236 Phgr1 5.25E−09 0.558407061 0.635 0.322 Aldh1b1 8.06E−06 0.557440384 0.466 0.25 Ace 3.93E−08 0.554965613 0.127 0 Tmigd1 3.55E−09 0.55155353 0.143 0 Vil1 1.01E−06 0.551098465 0.45 0.216 Sult1b1 4.49E−08 0.54573234 0.153 0.005 Ccl5 8.68E−08 0.544612494 0.122 0 Uqcrc1 4.05E−06 0.543715856 0.392 0.188 Gm21498 3.24E−06 0.542339507 0.529 0.293 Pdcd4 1.09E−10 0.538620646 0.312 0.067 Hnf4g 7.80E−07 0.533602425 0.185 0.024 Agpat2 5.98E−07 0.533276832 0.175 0.024 Xpnpep1 6.57E−07 0.531202684 0.206 0.038 Rfk 1.30E−05 0.525401438 0.36 0.144 Maf 8.88E−06 0.522184356 0.127 0.01 Khk 1.48E−05 0.519311747 0.153 0.024 Car8 3.64E−08 0.519192064 0.354 0.106 Nlrp6 1.10E−08 0.51574593 0.164 0.005 Cdca7 2.96E−06 0.514361605 0.185 0.029 Coro2a 1.72E−07 0.509456294 0.138 0.01 Xpnpep2 4.86E−05 0.508734097 0.106 0.005 Apoc3 3.44E−06 0.507147645 0.18 0.034 Tm4sf5 1.04E−05 0.506510188 0.265 0.111 Agt 1.36E−07 0.504633679 0.185 0.019 2010106E10Rik 9.14E−06 0.504516033 0.148 0.019 Gna11 1.82E−07 0.502564418 0.201 0.029 Me2 3.26E−10 0.502447092 0.254 0.038 Asph 1.06E−07 0.498901513 0.386 0.135 Slc51b 3.93E−08 0.498893766 0.127 0 Amn 6.23E−07 0.497927062 0.138 0.005 Rbp2 2.71E−07 0.493629472 0.143 0.005 Gm10936 6.50E−11 0.489589605 0.196 0.01 Ano6 1.78E−09 0.483434657 0.19 0.019 Mttp 3.42E−06 0.481033959 0.18 0.029 Pabpc1 7.43E−08 0.480498931 0.841 0.606 Mgst3 6.70E−07 0.47965119 0.333 0.13 Creb3l3 9.95E−06 0.478757185 0.111 0.005 Snord118 9.89E−07 0.478270728 0.296 0.091 n-R5-8s1 2.60E−11 0.477213392 0.175 0 Sel1l 1.68E−11 0.475890045 0.339 0.077 P4hb 3.48E−11 0.473083977 0.889 0.75 Sri 7.54E−09 0.471992839 0.407 0.149 B4galnt1 2.53E−07 0.466942661 0.206 0.038 Aldh9a1 0.000635305 0.465621436 0.196 0.077 Prlr 5.87E−07 0.463002595 0.138 0.005 Prr15 5.06E−11 0.462892291 0.392 0.115 Ivns1abp 1.10E−05 0.455338648 0.556 0.308 Glod5 7.56E−07 0.450811522 0.132 0.005 Cox6a1 2.95E−05 0.450622885 0.656 0.447 Mapk13 2.59E−05 0.448540988 0.243 0.072 Atp5d 3.76E−07 0.44814667 0.455 0.197 Cd74 8.16E−05 0.445384695 0.101 0.005 H2afv 2.67E−05 0.443257922 0.365 0.159 Ppp1r1b 0.000298994 0.44020946 0.249 0.091 Tmem59 1.50E−08 0.439241468 0.54 0.26 Aqp1 6.71E−06 0.438238419 0.291 0.101 Plac8 1.70E−06 0.438057927 0.693 0.481 Psmb10 1.18E−05 0.434360989 0.243 0.082 Ahnak 1.37E−06 0.432900374 0.106 0.01 Ppp1r14d 3.94E−05 0.432278825 0.138 0.019 Mep1a 6.23E−07 0.431438692 0.138 0.005 Klk1 0.00141784 0.430152287 0.122 0.024 Man1a 7.96E−07 0.429356647 0.275 0.072 Ndufa3 8.27E−05 0.429296854 0.392 0.202 Fam213b 5.14E−08 0.429263379 0.148 0.005 Map2k2 0.00043541 0.423775579 0.233 0.091 Mogat2 9.12E−07 0.420208529 0.106 0 Tmem120a 1.97E−05 0.41751037 0.127 0.019 Slc25a5 1.09E−06 0.416117714 0.746 0.572 Lsm2 0.002495442 0.415462138 0.111 0.024 Lgals4 7.47E−07 0.415061084 0.868 0.769 Gpr128 8.64E−07 0.413486524 0.127 0.014 Vdr 7.63E−06 0.412339435 0.143 0.014 Bcl2l15 8.37E−05 0.41126119 0.101 0.005 Alpi 1.98E−06 0.40984793 0.101 0 Mdh2 6.10E−05 0.405836853 0.392 0.212 Trp53inp1 2.98E−06 0.403353077 0.249 0.067 Car4 1.98E−06 0.403314629 0.101 0 Myo15b 4.23E−06 0.398700241 0.222 0.058 Hes1 0.001361387 0.397971035 0.228 0.087 Hsd17b11 1.65E−05 0.397016358 0.153 0.058 Golm1 1.64E−06 0.39487159 0.349 0.135 Vdac1 1.33E−05 0.394491186 0.28 0.101 Rbm47 2.33E−08 0.393474876 0.402 0.159 Lrba 3.11E−05 0.390948012 0.116 0.014 Acsl5 8.38E−05 0.390765407 0.222 0.072 Cs 0.001253395 0.390576902 0.233 0.101 Ms4a8a 5.36E−05 0.390074254 0.143 0.029 Klf5 0.001247316 0.389697895 0.222 0.091 Gpd1 0.001098308 0.38945621 0.18 0.058 Sult2b1 7.31E−05 0.389320415 0.101 0.005 Cox7a1 3.30E−05 0.387585592 0.106 0.01 Atp5b 4.19E−07 0.385794895 0.741 0.51 Chchd7 4.24E−05 0.385524129 0.291 0.115 H2-Q2 0.000550478 0.381917811 0.175 0.048 Vdac2 0.000600361 0.381917492 0.296 0.135 Ubl3 9.37E−08 0.381413149 0.302 0.091 Hspd1 0.003942912 0.380609278 0.349 0.202 Acox1 0.000611774 0.379594091 0.201 0.072 Atp5a1 1.18E−06 0.379498043 0.598 0.37 Ramp1 3.48E−07 0.377749721 0.37 0.144 Dusp1 9.55E−06 0.375874964 0.275 0.096 Lad1 0.000861872 0.375757898 0.201 0.077 Actn4 0.000120297 0.370280213 0.328 0.154 Atp5k 4.84E−08 0.3693736 0.524 0.255 Taldo1 0.000205287 0.366870125 0.466 0.269 2410015M20Rik 0.000101046 0.365838645 0.259 0.096 Styk1 5.34E−07 0.364713415 0.212 0.043 Mpp1 6.10E−05 0.364418368 0.148 0.034 Mgat4c 0.00012321 0.362713678 0.101 0.005 Clrn3 0.00124897 0.360568958 0.111 0.019 Gucy2c 1.00E−05 0.360208647 0.212 0.058 Slc12a2 1.30E−05 0.357673933 0.508 0.293 Ell2 3.92E−07 0.35672579 0.254 0.072 Reg3b 0.000111213 0.356094204 0.561 0.356 Prpsap1 0.00165382 0.355719227 0.148 0.053 Faah 0.002511093 0.354116242 0.111 0.024 Hmgcl 8.50E−05 0.353492089 0.132 0.038 Ubxn2a 4.70E−06 0.352849255 0.27 0.082 Hadh 8.14E−06 0.352437687 0.307 0.154 Pnrc1 0.00328913 0.352271477 0.217 0.087 Arf6 0.000338333 0.35191723 0.265 0.111 Gsr 5.42E−05 0.351862945 0.228 0.077 Etfa 1.75E−05 0.350637541 0.27 0.106 Lgals3 0.001089262 0.349966881 0.127 0.029 Tstd1 9.12E−07 0.349108292 0.106 0 Epcam 4.96E−05 0.348739761 0.852 0.668 Naip5 0.000158653 0.348352674 0.106 0.019 Abhd17c 0.000380818 0.347801117 0.132 0.034 Mgat4a 3.40E−06 0.347261458 0.175 0.038 Fosb 0.000748493 0.34637696 0.323 0.154 Sptssa 0.000443895 0.346066884 0.302 0.139 Cftr 0.000475678 0.344172836 0.122 0.019 Rpl41 2.46E−06 0.343548269 0.825 0.774 Efna1 0.000276603 0.342425524 0.164 0.043 Samhd1 0.000716801 0.340224417 0.122 0.029 Tmprss2 4.92E−05 0.340167759 0.439 0.236 Uqcrc2 1.16E−05 0.339484562 0.312 0.13 Sh3glb1 3.66E−07 0.339451718 0.328 0.13 Sidt2 4.64E−05 0.338809612 0.106 0.005 B2m 2.18E−06 0.338709962 0.624 0.423 Cobl 1.85E−05 0.338053322 0.18 0.038 Eps8l3 5.92E−06 0.336952586 0.233 0.067 Cyc1 0.001210813 0.336024668 0.259 0.115 Cryl1 0.000797843 0.335928912 0.101 0.019 Pccb 8.27E−08 0.334563979 0.238 0.058 Tkt 0.014546079 0.333591862 0.317 0.207 Lypd8 2.62E−06 0.331319233 0.577 0.327 Edem1 2.43E−05 0.329871174 0.243 0.072 Hagh 4.75E−06 0.329014544 0.212 0.053 Lyz2 8.82E−05 0.326985506 0.804 0.601 Dap 0.000106582 0.326795179 0.312 0.135 Sfxn1 0.009872151 0.325145567 0.201 0.087 Myh14 0.008668194 0.324263927 0.159 0.058 Smpdl3a 0.000282998 0.324029974 0.175 0.053 Fam174b 0.00048122 0.323778232 0.222 0.077 Gm24601 1.58E−09 0.323704332 0.148 0 Misp 0.010835316 0.323504586 0.175 0.082 Zzef1 0.010032456 0.322700043 0.101 0.024 Calm3 9.91E−05 0.322675306 0.317 0.139 Fahd1 0.000241362 0.321598446 0.148 0.034 Entpd7 1.89E−05 0.319727608 0.111 0.01 Serpinb1a 0.01616932 0.317900285 0.37 0.226 Jup 0.001389256 0.316634822 0.159 0.053 Csrp2 0.000446077 0.316243516 0.169 0.053 Pdha1 2.83E−06 0.316073056 0.339 0.144 Cap1 0.025029824 0.31523349 0.19 0.096 Ahcyl2 0.000303645 0.314865821 0.127 0.029 Tulp4 0.000105189 0.314158504 0.243 0.087 Gm10260 0.000202743 0.313419383 0.19 0.062 2-Mar 8.63E−06 0.311646492 0.354 0.168 Jun 0.00193883 0.31094902 0.672 0.505 Sppl2a 1.28E−05 0.310946885 0.36 0.163 Pgd 0.004689561 0.308578277 0.148 0.053 Zfyve21 0.000352105 0.3082869 0.138 0.029 Slc13a1 1.98E−06 0.308020729 0.101 0 Deptor 3.04E−05 0.307090565 0.143 0.024 Qsox1 7.84E−05 0.306665594 0.455 0.245 Slc25a15 4.10E−06 0.304116641 0.122 0.014 Tnfrsf1a 0.004530766 0.302312236 0.127 0.043 Cldn7 0.000579732 0.302041478 0.656 0.476 Stk11 0.015440853 0.30139002 0.132 0.048 Pxmp4 0.000212256 0.299765908 0.116 0.019 Add3 0.012709722 0.299738578 0.153 0.072 Tmbim6 1.30E−05 0.29957386 0.646 0.428 Ndufa10 0.000210867 0.298526344 0.185 0.072 Nadk 0.005939395 0.298399624 0.143 0.048 Tapbp 0.000527405 0.294741343 0.138 0.058 Ralgps2 0.000460055 0.294481536 0.127 0.024 Cox4i1 0.004003242 0.293346203 0.778 0.678 Mapk1 0.001303237 0.293271819 0.228 0.101 Specc1l 0.000406181 0.291989335 0.196 0.067 Rmdn3 0.002273752 0.291531342 0.101 0.019 Gng12 0.000615535 0.291180618 0.201 0.082 Il17rc 0.008351214 0.290611921 0.106 0.024 Kcne3 0.035168848 0.290073745 0.159 0.067 Perp 0.000122508 0.289832559 0.228 0.096 Arhgap21 0.002147713 0.289657036 0.116 0.024 Glud1 0.003813991 0.289341641 0.275 0.144 Pcmtd2 0.000133663 0.289334569 0.138 0.024 Pdxdc1 0.000611179 0.289301238 0.275 0.12 Syf2 0.000204932 0.287754737 0.159 0.062 Npepps 0.000210932 0.287490999 0.164 0.048 Ap2a2 5.77E−05 0.286049861 0.159 0.034 Ceacam1 0.012558374 0.285711887 0.185 0.082 Gm7861 5.09E−06 0.28566966 0.571 0.423 Ndufv1 0.000731802 0.285654675 0.217 0.087 Prodh 9.12E−07 0.28536933 0.106 0 Suclg1 0.001484541 0.284953462 0.296 0.154 Atp5e 2.01E−05 0.284538659 0.688 0.49 Tm9sf2 0.000226493 0.284242333 0.333 0.163 Azin1 0.000681563 0.28371138 0.228 0.091 Casp1 0.0128346 0.281796158 0.138 0.048 Cdhr2 0.001277173 0.281341383 0.217 0.087 Tsc22d3 0.000336506 0.28111833 0.106 0.014 Diap1 0.00036502 0.280817322 0.159 0.038 Aldh6a1 0.000127747 0.280771928 0.153 0.034 Ddx54 0.000262144 0.280593441 0.138 0.029 Adk 0.000427315 0.280112945 0.222 0.082 Sema4a 0.000836485 0.279603599 0.111 0.019 Pum1 0.046348529 0.279046058 0.122 0.053 Atg7 0.00773597 0.278616966 0.132 0.048 Gipc2 0.001821273 0.278357685 0.159 0.053 Bcar3 4.49E−05 0.278157211 0.132 0.024 Mvp 0.006999775 0.277281462 0.122 0.034 Ifi30 0.006205503 0.277151701 0.116 0.038 Rac1 1.45E−06 0.276928263 0.28 0.106 Plekhb2 1.15E−07 0.276052595 0.201 0.043 Iqgap2 0.0013389 0.275988331 0.116 0.029 Lman1 6.25E−06 0.275922903 0.397 0.197 Osr2 0.000621614 0.275671454 0.106 0.014 Nucb2 0.000164379 0.274634584 0.386 0.197 Ak2 0.00687328 0.274187748 0.312 0.178 Atp5c1 0.002880814 0.274042138 0.513 0.389 Gpa33 0.046607098 0.273985868 0.175 0.106 Copa 0.000526397 0.273955995 0.259 0.115 Ndufb8 0.006740515 0.273190659 0.402 0.25 Sdha 0.005840515 0.272878213 0.265 0.135 Riok3 0.002258585 0.272636128 0.153 0.053 Clca4 0.002111404 0.272622559 0.291 0.149 Rnf128 3.99E−07 0.271082123 0.503 0.274 Camk2d 0.000434015 0.270550821 0.132 0.029 2010107E04Rik 0.001866922 0.270511937 0.619 0.428 Hnf4a 0.002383177 0.270376795 0.228 0.106 Unc93b1 3.79E−05 0.270366067 0.111 0.01 Cda 0.013682109 0.268416519 0.101 0.024 Wasl 0.00196066 0.268014022 0.18 0.067 Gne 0.000210937 0.267730362 0.201 0.062 Chchd3 0.002554413 0.266784765 0.222 0.101 Bola3 0.132044858 0.266144467 0.122 0.058 Ccdc107 0.002422551 0.265968784 0.122 0.048 Akap8 0.008747812 0.265357404 0.116 0.038 Hjurp 0.178462987 0.264089732 0.111 0.058 Lta4h 0.036965722 0.264026193 0.175 0.082 Tmem54 1.61E−05 0.263806428 0.18 0.062 Ddx47 0.004818384 0.263691556 0.101 0.019 Surf4 0.000298793 0.263678254 0.402 0.221 Kit 7.85E−08 0.263669741 0.28 0.091 Sucla2 0.006604643 0.262674028 0.18 0.082 Cep350 0.00096944 0.262051265 0.132 0.038 Wnt3 0.000977386 0.26198011 0.217 0.087 Pdcd6 0.007882918 0.25818866 0.222 0.115 Pim3 3.35E−05 0.258174011 0.286 0.115 Cldn15 0.000187162 0.257624763 0.349 0.192 Itm2b 0.000223028 0.257321318 0.571 0.375 Slc31a1 0.004356272 0.257137521 0.169 0.062 Vaultrc5 0.001619244 0.257017214 0.185 0.082 Defa5 0.005601392 0.256972377 0.698 0.572 Samd5 5.45E−08 0.256637806 0.143 0.01 Aldh2 0.00066891 0.256489269 0.116 0.029 Stat6 0.003478488 0.256235435 0.122 0.029 Canx 0.00040178 0.256007952 0.598 0.404 Smim6 6.80E−08 0.255781064 0.296 0.096 Vapa 0.000226208 0.255554437 0.291 0.135 Wdr1 0.004423034 0.255433876 0.201 0.096 Mgst2 0.000188956 0.254791701 0.259 0.111 Klf10 0.012020168 0.254344833 0.164 0.067 Myb 0.028335838 0.253500318 0.101 0.029 Serpinb6a 0.005531695 0.253468724 0.349 0.202 Efcab4b 0.002091294 0.252975069 0.127 0.029 Tfrc 0.000422437 0.251901024 0.127 0.043 Ppard 0.000896655 0.251380411 0.111 0.019 Tfg 1.95E−05 0.250724854 0.238 0.101 Fam213a 2.53E−09 0.250180706 0.407 0.163 Cox7a2l 0.017484589 −0.252140376 0.27 0.322 Srebf2 0.011510883 −0.254567514 0.048 0.115 Tubb5 0.129347951 −0.259916799 0.275 0.341 Gm5160 0.073566054 −0.260849627 0.048 0.12 Npm1 0.009802281 −0.261222987 0.418 0.514 Rps15a 6.50E−07 −0.261768917 0.725 0.856 Cnn3 0.026069066 −0.266341458 0.085 0.149 Rpl11 0.02518531 −0.275194507 0.079 0.13 Rpl21 0.013458619 −0.276391478 0.058 0.115 Sec61g 0.014267567 −0.276477428 0.058 0.115 Prdx4 0.031550414 −0.280664075 0.069 0.12 Ndufa6 0.000225184 −0.281719307 0.545 0.649 Polr2e 0.058371858 −0.282416849 0.116 0.173 Gm10704 0.003253615 −0.289029224 0.048 0.115 Ythdc1 0.09564442 −0.28958559 0.074 0.125 Rps3 7.94E−11 −0.289729383 0.868 0.928 Nr2c2ap 0.000588514 −0.293271871 0.042 0.101 Areg 0.001281208 −0.298928777 0.053 0.135 Zfp36l1 0.000240351 −0.29934516 0.085 0.144 Maged1 0.003332676 −0.30045974 0.048 0.101 Tmem14c 0.002306995 −0.304323857 0.111 0.168 Eef1d 0.001371079 −0.305433379 0.222 0.284 Rpl23a 0.062152778 −0.305851719 0.069 0.135 Pbdc1 0.025943464 −0.306212432 0.042 0.106 Orc5 0.056455039 −0.30646476 0.116 0.192 Irf2bp2 0.008329455 −0.307736405 0.106 0.173 Rps23 0.011739843 −0.308446698 0.069 0.135 Ten1 0.102160524 −0.309709144 0.101 0.159 Rpl13a-ps1 0.042009656 −0.310152675 0.085 0.159 Mif 0.018013509 −0.310948239 0.106 0.178 Rpl21-ps4 0.000240118 −0.311183162 0.042 0.115 Sc4mol 0.007711873 −0.311224746 0.111 0.183 Rpl37 0.008770113 −0.3115343 0.365 0.462 Polr2f 0.000273658 −0.312235393 0.228 0.293 Rpl17 0.006815832 −0.312820054 0.053 0.12 2310036O22Rik 0.010330838 −0.315652547 0.085 0.144 Bri3 0.014926152 −0.317141505 0.09 0.154 Dbi 0.001079677 −0.317560635 0.54 0.611 Fryl 0.010593255 −0.318541718 0.085 0.144 Rps10-ps1 0.028097021 −0.318863607 0.233 0.312 U2surp 0.027164055 −0.319014849 0.111 0.173 Smoc2 0.007238828 −0.319778202 0.238 0.303 Psmb7 0.006477049 −0.320215106 0.037 0.13 Gstp1 0.013296427 −0.321690138 0.132 0.221 Srp9 3.78E−05 −0.322697933 0.333 0.385 Tuba4a 0.016637477 −0.322905383 0.101 0.159 Ifl27 0.015397997 −0.322923537 0.042 0.106 Tm2d1 0.05115425 −0.325196427 0.079 0.135 Gstm1 0.000230566 −0.325940509 0.026 0.135 Gm10288 0.016862232 −0.32672543 0.058 0.139 Eid1 0.004080842 −0.327986425 0.063 0.12 Nfib 0.003840857 −0.332070479 0.048 0.106 Fkbp11 0.001702597 −0.33457054 0.201 0.274 Gadd45b 0.005428897 −0.335179663 0.053 0.115 Gtf2i 0.005136519 −0.33667399 0.09 0.168 Rpl19 0.011486209 −0.338013065 0.143 0.236 Timm13 0.001871889 −0.338574841 0.265 0.327 Itgb1 0.036462386 −0.343180778 0.159 0.231 Brk1 0.01403406 −0.346372631 0.132 0.197 Slc20a1 0.002705833 −0.3488653 0.021 0.111 Cxadr 0.004298945 −0.350462975 0.127 0.178 Nhp2l1 0.00822258 −0.352218539 0.021 0.101 Phpt1 0.0029264 −0.352720363 0.058 0.12 Hsbp1 0.000823419 −0.353008576 0.169 0.236 Swi5 1.51E−05 −0.354053685 0.212 0.264 Tcp1 0.001071065 −0.357264628 0.19 0.279 Slirp 0.027120843 −0.359162885 0.201 0.26 Tmem176b 0.014638728 −0.360250299 0.18 0.26 Tsc22d1 0.000310827 −0.362193796 0.185 0.25 Rpl10 0.005810772 −0.365229817 0.063 0.168 Cldn3 0.000169145 −0.3667166 0.423 0.486 Snhg3 0.010138043 −0.367572874 0.053 0.135 Nisch 0.005919767 −0.376326043 0.069 0.139 Rps21 4.71E−07 −0.376428799 0.725 0.837 Rpl29 0.002651795 −0.376516598 0.243 0.298 Eif4g1 0.002722413 −0.376609408 0.28 0.361 Aplp2 0.000531071 −0.378339699 0.132 0.202 Avpi1 4.78E−05 −0.379758207 0.048 0.106 Nedd8 0.000377334 −0.380703757 0.217 0.269 Rpl35 0.000724596 −0.381303013 0.508 0.625 Krt23 0.000800174 −0.38220357 0.074 0.159 Rnf6 0.001260028 −0.384243793 0.063 0.12 Rpl32 2.57E−17 −0.384437253 0.91 0.981 Tmem57 0.000405747 −0.386349148 0.053 0.125 mt-Nd6 0.016053176 −0.389263233 0.095 0.173 Gm12728 0.000351127 −0.389554077 0.021 0.106 Ngfrap1 0.001609665 −0.390367209 0.079 0.13 Thyn1 0.008380408 −0.39170097 0.032 0.101 H3f3a 0.004457828 −0.392346385 0.18 0.269 Ssb 0.0001136 −0.39357373 0.275 0.327 Tecr 0.000573426 −0.393628314 0.138 0.226 Wdr89 0.000939611 −0.393703708 0.233 0.361 Ttr 0.003337606 −0.395342766 0.026 0.101 Ostc 0.000377159 −0.396743193 0.275 0.365 Rpl13a 7.09E−11 −0.397237135 0.825 0.938 Cpe 9.63E−05 −0.397741526 0.005 0.106 Tpsg1 0.004260073 −0.398698859 0.048 0.135 Gm9843 2.85E−06 −0.401098423 0.481 0.596 1110038B12Rik 0.013164847 −0.402047429 0.19 0.293 Commd3 0.001200104 −0.402077169 0.101 0.183 Tmem205 0.004058066 −0.402193663 0.101 0.197 Calml4 0.000206327 −0.40286878 0.328 0.385 Tm4sf4 9.64E−07 −0.403129844 0.376 0.433 Rbx1 0.000414636 −0.405344456 0.169 0.279 Rpl31 0.012997575 −0.406077236 0.106 0.212 Pomp 0.000173576 −0.40754857 0.19 0.26 Psat1 0.000502605 −0.407965285 0.021 0.115 Rgcc 0.00096964 −0.408602614 0.101 0.154 Atf4 0.000403041 −0.408615916 0.36 0.438 Fundc2 0.007364425 −0.409271455 0.09 0.183 Strn3 0.000337646 −0.409440929 0.111 0.168 Elf4ebp1 0.000507077 −0.409543936 0.132 0.183 Gm9396 3.28E−06 −0.409551355 0 0.101 Atf5 3.28E−06 −0.411534575 0 0.101 Hn1 0.000806639 −0.412677099 0.196 0.269 Rpl14 3.91E−09 −0.413504979 0.667 0.88 D10Bwg1379e 3.85E−06 −0.41494752 0.069 0.135 Hmgcr 0.011028758 −0.41849862 0.079 0.135 Chchd2 1.85E−06 −0.418713149 0.556 0.644 Gm24146 4.45E−05 −0.41888405 0.005 0.106 Atox1 0.005490355 −0.419855051 0.153 0.216 Gstm5 0.000694529 −0.420074174 0.079 0.163 mt-Nd2 4.24E−07 −0.420870803 0.683 0.837 2700060E02Rik 0.000176909 −0.421110265 0.185 0.279 Gadd45g 0.001950316 −0.422570759 0.265 0.332 Ndufa1 0.000579309 −0.425214056 0.249 0.346 Lect2 8.44E−07 −0.425590616 0 0.111 Prdx2 7.18E−05 −0.427400479 0.307 0.385 0610009D07Rik 0.000129747 −0.431551957 0.122 0.221 Echdc2 0.001345941 −0.432901186 0.021 0.106 Srp14 3.41E−05 −0.434110934 0.169 0.236 Lrrc26 0.000269847 −0.43462566 0.106 0.192 Ltn1 4.43E−05 −0.43496069 0.074 0.173 Tceb2 0.000549685 −0.438016411 0.254 0.356 Hist1h1c 0.000416334 −0.438205493 0.09 0.154 Gm25911 0.000203714 −0.4389797 0.021 0.13 Rdh10 0.002218378 −0.439024801 0.032 0.106 Polr3k 0.003914754 −0.439369247 0.079 0.192 Adh1 0.000947453 −0.439537545 0.021 0.115 Selm 2.05E−06 −0.439723493 0.418 0.476 Prdx1 1.30E−06 −0.440301939 0.709 0.784 Mt2 0.00456606 −0.440867663 0.079 0.163 Eif3m 4.93E−05 −0.441195248 0.159 0.212 Gm8420 7.29E−06 −0.441299956 0.048 0.13 Gm6139 4.26E−07 −0.443757087 0 0.115 Rps13 0.00057086 −0.444545236 0.053 0.173 Fdps 0.002872595 −0.44477163 0.048 0.154 Gm9493 0.000158185 −0.445937708 0.048 0.144 Ywhaq 0.000629845 −0.448390041 0.127 0.24 Cd81 0.002047566 −0.451319262 0.143 0.245 Gas5 1.71E−05 −0.454302947 0.455 0.635 H2afz 0.007854924 −0.45441755 0.074 0.173 Skp1a 3.87E−06 −0.455711713 0.37 0.423 Ncl 9.61E−07 −0.457511022 0.577 0.639 Hmgcs1 0.000290879 −0.458974021 0.18 0.25 Gm10132 7.44E−05 −0.459725739 0.016 0.111 Ranbp1 0.000528075 −0.460830613 0.238 0.341 Rps11 1.24E−06 −0.46209607 0.593 0.74 mt-Atp6 0.001240713 −0.462281332 0.101 0.231 Sec61b 1.18E−07 −0.462312239 0.646 0.736 Taf1d 0.013277287 −0.462875628 0.116 0.192 Grcc10 0.000332073 −0.463270318 0.042 0.12 Cfl1 1.94E−05 −0.463334089 0.233 0.322 Prom1 2.67E−05 −0.463399463 0.143 0.236 Rps17 0.00116106 −0.464881009 0.058 0.173 Ubl5 8.96E−05 −0.464892598 0.291 0.38 Rpl6 6.52E−05 −0.465214038 0.196 0.332 Hbegf 0.000104344 −0.466684197 0.106 0.183 Dynll1 2.57E−07 −0.46756004 0.27 0.394 Btf3 0.000134943 −0.467926409 0.185 0.284 Sec11c 1.02E−07 −0.473369926 0.476 0.558 Oaz1 8.09E−05 −0.475982534 0.339 0.49 Phgdh 2.44E−05 −0.481364965 0.016 0.125 Psmb6 0.000319976 −0.482323069 0.254 0.351 Selk 1.75E−07 −0.482556045 0.296 0.394 Rps9 7.39E−13 −0.483566949 0.778 0.942 Tomm20 0.000132435 −0.490044399 0.063 0.202 Lsr 2.46E−05 −0.491175809 0.27 0.375 Atp5g1 8.08E−05 −0.492013593 0.116 0.216 Psmd8 6.76E−06 −0.492661387 0.185 0.26 Snrpg 0.001572527 −0.493223107 0.143 0.25 Ptma 8.07E−06 −0.493817227 0.413 0.524 Aldoa 4.69E−07 −0.493870974 0.265 0.322 Rps27a 6.85E−05 −0.4972725 0.143 0.264 Rpl23a-ps3 1.15E−06 −0.500902127 0.005 0.139 Rpl10a 0.00028653 −0.504079744 0.106 0.25 Tmed6 2.07E−08 −0.506835091 0.439 0.51 Laptm4b 1.64E−05 −0.508853003 0.053 0.13 Bud31 1.46E−06 −0.509698976 0.127 0.197 Gm6576 6.58E−05 −0.510464331 0.085 0.25 Hsp90aa1 0.000105567 −0.511293723 0.217 0.37 Hmgb2 0.00044436 −0.512039439 0.159 0.226 Rpl22l1 6.48E−06 −0.513112107 0.471 0.596 Atp6v0e 4.01E−05 −0.513115296 0.169 0.24 Gm10269 5.18E−05 −0.513419769 0.185 0.312 Rpl10-ps3 7.01E−05 −0.515446334 0.032 0.154 Son 6.18E−06 −0.516770037 0.286 0.346 Pkm 0.00019381 −0.521392815 0.19 0.341 Rpl12 0.000101383 −0.521536295 0.079 0.216 Slc25a4 0.000186223 −0.527207956 0.037 0.168 1810037I17Rik 1.54E−05 −0.529384464 0.212 0.269 Pdgfa 8.68E−05 −0.532795772 0.063 0.178 Ssr4 1.02E−11 −0.533813325 0.661 0.712 Tmem167 1.35E−06 −0.536054534 0.164 0.245 Gip 4.57E−05 −0.537319439 0.021 0.115 Gng5 7.65E−06 −0.538609306 0.164 0.279 Nme1 8.52E−06 −0.539926697 0.323 0.514 Acta1 0.000254708 −0.541387123 0.016 0.12 Rps24 2.03E−21 −0.545654318 0.852 0.962 Nop10 5.91E−06 −0.546337145 0.302 0.409 Cdk4 1.20E−05 −0.547122866 0.196 0.332 Rps3a1 2.41E−10 −0.547636784 0.603 0.788 Rpl36al 3.00E−07 −0.552987884 0.434 0.596 Pcna 6.64E−06 −0.557475861 0.032 0.178 Rps27l 1.29E−09 −0.558161739 0.63 0.745 Naca 2.28E−06 −0.559060194 0.365 0.514 Cystm1 2.14E−05 −0.560521007 0.27 0.49 Eef1b2 5.73E−11 −0.561211449 0.635 0.827 Rps15 7.52E−09 −0.563493746 0.571 0.707 Gsta4 0.000376155 −0.565132131 0.048 0.154 Tpm4 1.18E−05 −0.572677052 0.111 0.24 Plk2 5.10E−07 −0.575972557 0.016 0.13 Atrx 4.88E−06 −0.577584592 0.169 0.264 Rpl18 5.72E−07 −0.577961954 0.291 0.471 Pglyrp1 4.66E−08 −0.580517035 0.286 0.447 Rpl38 1.59E−08 −0.58124534 0.54 0.673 mt-Nd5 3.08E−08 −0.583013223 0.598 0.726 Cstb 2.54E−06 −0.588440967 0.127 0.264 Tnfrsf12a 6.52E−06 −0.593759924 0.026 0.159 Rpl18a 3.19E−08 −0.594960202 0.376 0.587 mt-Co1 4.09E−14 −0.596199034 0.72 0.894 Ftl1 1.25E−07 −0.596348892 0.201 0.341 Rpl27a 2.96E−06 −0.597795638 0.196 0.375 Pebp1 1.11E−05 −0.602051355 0.085 0.236 Gm6472 1.11E−06 −0.605115885 0.037 0.178 Ubb 8.67E−10 −0.606892668 0.534 0.683 Myl12a 5.89E−05 −0.607360494 0.233 0.375 Rps2 1.55E−17 −0.607915911 0.725 0.913 Krt7 7.00E−08 −0.608551206 0.185 0.327 Tac1 1.32E−08 −0.609466655 0 0.139 Ccdc34 9.24E−07 −0.610192214 0.148 0.245 Nme2 4.16E−07 −0.616087733 0.037 0.212 Spcs1 1.98E−10 −0.624977292 0.296 0.394 Rpl5 3.14E−07 −0.633252154 0.032 0.202 mt-Cytb 9.60E−18 −0.633457589 0.878 0.947 Gnb2l1 1.40E−16 −0.634921488 0.725 0.851 Gcg 3.92E−07 −0.636343125 0.016 0.168 Hmgn1 2.55E−05 −0.636993308 0.164 0.284 Cd63 1.62E−14 −0.637719602 0.593 0.721 Rpl26 8.42E−17 −0.638634723 0.735 0.923 Rps5 5.27E−21 −0.646605873 0.862 0.962 Rps25 1.81E−07 −0.652872931 0.228 0.423 H3f3b 1.69E−13 −0.659838522 0.545 0.688 Atp6v1f 8.30E−07 −0.664009401 0.169 0.312 Ssr2 7.06E−09 −0.664712565 0.354 0.476 Atp6v1g1 4.97E−06 −0.664760371 0.095 0.255 Rps6 2.05E−07 −0.665915434 0.063 0.274 Rpl23 8.44E−10 −0.669667798 0.429 0.668 Cyp2c55 4.42E−07 −0.674226292 0.005 0.144 Pla2g1b 8.84E−11 −0.67953062 0 0.173 Cst3 1.67E−11 −0.682317075 0.339 0.438 Gm26917 1.35E−05 −0.683305761 0.048 0.178 Romo1 1.54E−07 −0.699449376 0.164 0.37 Myl6 6.18E−09 −0.69964038 0.106 0.288 Ctsl 1.33E−08 −0.703093615 0.053 0.245 Cyr61 1.00E−08 −0.704444878 0.063 0.231 Rpl30 1.25E−09 −0.70998512 0.254 0.462 Rnf32 5.41E−06 −0.710130688 0.111 0.221 Rplp1 3.38E−30 −0.712756027 0.878 0.981 Defa25 1.61E−10 −0.715705986 0.185 0.399 Ang6 5.79E−11 −0.716221276 0.212 0.351 Rpl13 2.27E−14 −0.717649203 0.561 0.788 Actg1 1.92E−10 −0.724955082 0.063 0.269 Rps16 3.84E−07 −0.729478717 0.175 0.37 Tuba1a 2.94E−09 −0.73434991 0.021 0.168 Rps10 1.03E−18 −0.737307591 0.614 0.827 Rps8 5.48E−14 −0.742402719 0.503 0.692 Rpl3 2.14E−10 −0.750557432 0.333 0.62 Sox4 3.03E−08 −0.760506904 0.069 0.245 Fkbp3 8.56E−07 −0.76976704 0.217 0.365 1810022K09Rik 1.45E−08 −0.787524184 0.138 0.337 Chga 1.32E−10 −0.791039349 0.021 0.221 Lrrc58 2.42E−10 −0.792043496 0.222 0.476 Rpsa 6.39E−10 −0.795078971 0.228 0.495 Gm9765 2.36E−13 −0.825289527 0.206 0.413 mt-Nd1 8.58E−29 −0.850345382 0.852 0.986 Ifitm2 1.15E−12 −0.865114602 0.228 0.418 Cfi 8.89E−13 −0.876969132 0.016 0.226 Ppia 2.89E−12 −0.893106102 0.058 0.337 Cyp2e1 2.33E−10 −0.918234535 0.026 0.231 Eef1a1 1.44E−31 −0.932185435 0.772 0.933 Cck 1.71E−13 −0.956946027 0.016 0.269 Fxyd3 1.64E−14 −0.960305221 0.265 0.514 Sct 3.37E−09 −0.969003141 0.196 0.433 Ghrl 1.83E−10 −0.969586007 0 0.168 Gm10275 2.62E−15 −0.983530061 0.095 0.389 Rps4x 8.06E−17 −0.985916347 0.228 0.567 Scd2 9.20E−15 −1.024887641 0.079 0.394 Rpl7a 1.27E−16 −1.037579581 0.116 0.466 Ang2 4.01E−18 −1.051661404 0.132 0.438 Gm8730 5.84E−19 −1.059036053 0.206 0.606 Thbs1 3.11E−17 −1.062661826 0.217 0.442 Rps20 2.28E−38 −1.063543475 0.656 0.928 Rnase1 5.09E−13 −1.06995887 0.164 0.428 D17H6S56E−5 1.33E−15 −1.099963647 0.185 0.476 Rps7 4.89E−26 −1.161473081 0.365 0.76 Tmsb10 3.28E−25 −1.199574969 0.333 0.683 Clu 4.67E−18 −1.212913464 0.005 0.298 S100a11 2.36E−20 −1.226604206 0.053 0.438 Uba52 4.77E−30 −1.28447217 0.259 0.736 Cldn4 5.51E−25 −1.293526661 0.153 0.5 Ifitm3 4.43E−22 −1.306612102 0.048 0.452 Gm23935 6.91E−34 −1.326558771 0.762 0.913 Malat1 1.04E−43 −1.360749436 0.825 0.995 Rpl7 1.59E−37 −1.409066357 0.349 0.846 Ifitm1 8.32E−28 −1.434635185 0 0.404 S100a6 5.28E−24 −1.444056948 0.101 0.495 Xist 9.33E−33 −1.583925327 0 0.462 Tpt1 3.19E−48 −1.661520782 0.286 0.798 Chgb 5.51E−36 −1.908187675 0.011 0.519

TABLE 2 Reference gene lists used in single-cell analyses Respiratory Electron Proteome Down Proteome Down Wnt_KEGG Reactome_Notch Transport Proteome Up 1-164 Proteome Up 165-328 1-152 153-303 APC ADAM10 COX1 Ern2 Cracr2a Brwd3 Esf1 APC2 ADAM17 COX2 Mecp2 Mmp7 Cd44 Gnat3 AXIN1 APH1A COX3 Plcb1 Fhdc1 Ndufaf5 Shank3 AXIN2 APH1B COX4I1 Pla2g1b Mtus2 Ppig Srek1ip1 BTRC ARRB1 COX5A Ggh Plb1 Lrp2 Srrm1 CACYBP ARRB2 COX5B Npc2 Manf Mllt6 Prune2 CAMK2A ATP2A1 COX6A1 Pmfbp1 Ang4 Slfn9 Mrpl43 CAMK2B ATP2A2 COX6B1 Cpq Zbtb38 Gm13251 Cluh CAMK2D ATP2A3 COX6C Wif1 Tmc5 Ski Scin CAMK2G B4GALT1 COX7A2L Lemd3 Gsdma2 Coro2a Adck3 CCND1 CCNC COX7B Phf2 Ush2A Zcchc7 Adck3 CCND2 CCND1 COX7C Insrr Sct Mylk Dmbt1 CCND3 CDK8 COX8A Nupr1 Lgals3bp Zfp40 Scarb1 CER1 CNTN1 CYC1 Ak1 Clu Ptprb Mme CHD8 CREBBP CYCS Celsr2 Eml1 Cttnbp2 Ces1e CHP CUL1 CYTB Hgfac Cyp2e1 Mgst1 Fau CHP2 DLK1 ETFA Dnajc12 Rcn1 Fam151b Hspe1 CREBBP DLL1 ETFB Ctsf Smpd1 Gm8973 Ugt1a6 CSNK1A1 DLL4 ETFDH Dach1 Scg2 Olfm4 Nqo1 CSNK1A1L DNER LOC651820 Pcsk1n Hivep1 Zranb2 Ces2b CSNK1E DTX1 LOC727947 Dbn1 Aplp1 Ugt1a8 Zfp677 CSNK2A1 DTX2 MTND5P10 Poll Serpina1c Bud31 Clta CSNK2A2 DTX4 ND1 Dnaja4 Cpe AU019823 L1cam CSNK2B E2F1 ND2 Pfn2 Bmp1 Ces2g Rab35 CTBP1 E2F3 ND3 Cryba2 Ang3 Tstd1 Dna2 CTBP2 EIF2C1 ND4 Cpn1 Anpep Khk Wdr43 CTNNB1 EIF2C2 ND4L Herpud1 S100a13 Prss32 Rps9 CTNNBIP1 EIF2C3 ND5 Ammecr1 Serping1 Nolc1 Rps27 CUL1 EIF2C4 ND6 Slc9a3r2 Serf2 Ythdc1 Rpl10 CXXC4 EP300 NDUFA1 Dpp7 Cplx2 Slc4a4 Rpl35 DAAM1 FBXW7 NDUFA10 Gsdma Nucb2 Ddias Rps27l DAAM2 FURIN NDUFA11 Maged2 Ptprn2 Nlrp6 Rpl36 DKK1 HDAC1 NDUFA12 Fn3k Evl Atp4a Brd2 DKK2 HDAC10 NDUFA13 Sgsh Tbx3 Wdhd1 Eri1 DKK4 HDAC11 NDUFA2 Wbp5 Pcsk1 Ttll12 Dek DVL1 HDAC2 NDUFA3 Gmpr Ufm1 Zfp709 Gvin1 DVL2 HDAC3 NDUFA4 Crip2 Cirbp Dnajc19 Nucks1 DVL3 HDAC4 NDUFA5 Hmgn3 Dock4 Zc3h18 Lig3 EP300 HDAC5 NDUFA6 Srpr Rnf216 Dctd Clic6 FBXW11 HDAC6 NDUFA7 AY761184 Rp1 Supt16 Cdca8 FOSL1 HDAC7 NDUFA8 Cyp2c55 Wfs1 Gm4794 Ces2e FRAT1 HDAC8 NDUFA9 Clca1 Maz Tcof1 Gpr128 FRAT2 HDAC9 NDUFAB1 Prss23 Kmt2a Noc2l Eif1ax FZD1 HES1 NDUFB1 Gabra4 Gcg Vdac3 Kat6b FZD10 HES5 NDUFB10 Cep83 Gck Pbld1 Pisd FZD2 HEY1 NDUFB2 Nts Hrsp12 Arg2 Maob FZD3 HEY2 NDUFB3 Zswim7 Ccl9 Reg3a Clic5 FZD4 HEYL NDUFB4 Mansc1 S100a11 Chek1 Tbc1d4 FZD5 HIF1A NDUFB5 Clps Gip Fxn Ncaph FZD6 JAG1 NDUFB6 Cuta Prox1 Aldh1a7 Ttc22 FZD7 JAG2 NDUFB7 Ftl1 Anxa5 Rab33b Cps1 FZD8 JUN NDUFB8 Sytl2 Igfbp2 Sdc4 Ptcd1 FZD9 KAT2A NDUFB9 Sytl2 Scg3 Suv39h1 Zim1 GSK3B KAT2B NDUFC1 Ddah2 Ina Aurkb Yipf4 JUN LFNG NDUFC2 Sntb1 Cdkn1b Mpzl2 Cwc22 LEF1 LOC441488 NDUFS1 Vmp1 Plin2 Fgfbp1 Ccdc28a LOC728622 LOC728030 NDUFS2 Homer3 Hist1h1a Slc25a17 Clasrp LRP5 MAML1 NDUFS3 Ly6e Alox15 Myo1a Gnal LRP6 MAML2 NDUFS4 Pdia5 Fbln2 Papss2 Rdh1 MAP3K7 MAML3 NDUFS5 Tor1aip1 Thbs1 Rdh7 Cyp2d26 MAPK10 MAMLD1 NDUFS6 Bicd2 Ahsg Gmnn Card11 MAPK8 MFNG NDUFS7 Sncb Marcksl1 Parp2 Akr1c18 MAPK9 MIB1 NDUFS8 Dnah8 Mt3 Afp Zg16 MMP7 MIB2 NDUFV1 Spats2l Ets1 Mt2 Krtcap3 MYC MOV10 NDUFV2 Ugt2b38 Chga Mt1 Tinf2 NFAT5 MYC NDUFV3 Scgn Serpina1b Tk1 Cbr3 NFATC1 NCOR1 SDHA Plcb4 Ang Apoa4 Itpka NFATC2 NCOR2 SDHB Oas3 Cst3 Ckm Znf768 NFATC3 NCSTN SDHC Slc12a8 Vim Tyms Plbd1 NFATC4 NEURL SDHD Selm Muc13 Ncl Ak6 NKD1 NOTCH2 UQCR11 Pla2g15 Nefh Rrm2 Ces1d NKD2 NOTCH3 UQCRB Gdap1l1 Ctsd Otc Naa40 NLK NOTCH4 UQCRBP1 Gpld1 Lyz1 Atp1b1 Lmcd1 PLCB1 NUMB UQCRC1 Sh3kbp1 Wnt3 Rpl27a Ca9 PLCB2 POFUT1 UQCRC2 Ppp1r14c Chgb Rps16 PLCB3 POGLUT1 UQCRFS1 Cd177 Hmox1 Srp14 Impa2 PLCB4 PSEN1 UQCRH Ssbp1 Map1b Slc7a2 Nifk PORCN PSEN2 UQCRHL Ctbs Anxa6 Dao Nsmce2 PPARD PSENEN UQCRQ Hid1 Scg5 Tcea3 Tipin PPP2CA RAB6A Pitpnc1 Gusb Rps2 Depdc7 PPP2CB RBPJ Irak3 Fn1 Gna12 Ces1f PPP2R1A RBX1 Pom121 H1f0 Rpl3 St3gal4 PPP2R1B RFNG Dync2li1 Anxa1 Psmb9 Aldob PPP2R5A RPS27A Habp2 Nudt10 Adssl1 Smc1b PPP2R5B RPS27AP11 Aspm Cck Casp1 Ddb2 PPP2R5C SEL1L Liph Nefm Hmgb2 Nrf1 PPP2R5D SKP1 Celf3 Nefl Pou2f3 Rsl24d1 PPP2R5E SNW1 Btbd7 Sod1 Chd1 Gins4 PPP3CA ST3GAL3 Myt1 Ttr Vhl Fars2 PPP3CB ST3GAL6 Kctd2 Ctsl Reg1 Rnps1 PPP3CC TBL1X Lancl3 Ada Pla2g4a Cdca3 PPP3R1 TBL1XR1 Nhlrc3 Rnase1 Rpia Mrps18a PPP3R2 TFDP1 Cnst Tcn2 Vdr Mrps5 PRICKLE1 TLE1 Gatsl2 Lect2 Brca1 Mrpl16 PRICKLE2 TLE2 Rnase4 Agr2 Shmt1 Acss1 PRKACA TLE3 Defa22 Itln1 Fabp6 Aadac PRKACB TLE4 Parp12 Tmem131 Rpl9 Mrpl15 PRKACG TMED2 Fgd2 Snca Plcb3 Pno1 PRKCA TNRC6A Sgsm1 Serpini1 Efnb2 Mrpl51 PRKCB TNRC6B Qsox1 Anxa3 Dmpk Fam195a PRKCG TNRC6C Dzip1 Ift81 Fabp2 Mrpl20 PRKX TP53 Hspa13 Ptpn9 Aqp4 Rpl21 PSEN1 UBA52 Gskip Cyp3a25 Atp5e Zwint RAC1 Gns Reg3g Cyb5a Snx24 RAC2 Zc3hav1l Lfng Rps20 Fam133b RAC3 Nfasc Stxbp1 Rab10 Gemin7 RBX1 Topors Cacna2d1 Rpl27 Mgme1 RHOA Thbs1 Capn2 Rpl37a Cenpv ROCK1 Mtdh Hk2 Rnd3 Mrps28 ROCK2 Cpm Stim2 Abat Rpl15 RUVBL1 Slit1 Ank3 Timm8b Cmss1 SENP2 Cadps Ank3 Rps7 Lipt2 SFRP1 Tppp Prom1 Rps8 Mrto4 SFRP2 Mroh2b Mtss1 Rps15a Ube2c SFRP4 Slc39a4 Gimap9 Rps23 Rpl34 SFRP5 Rph3al Zfp407 Rps18 Zdhhc21 SIAH1 Syne1 Sgsm3 Hist1h4a Msra SKP1 Tiam2 Ktn1 Rpl23 Mrpl2 SMAD2 Atp8b3 Pam Rps24 Ociad2 SMAD3 Sarm1 D3Ertd254e Rps25 1810009A15Rik SMAD4 Ttbk1 Pcdhb12 Rps26 Knstrn SOX17 Crmp1 Ccdc149 Polr2l 42627 TBL1X Zranb3 Fcgbp Rpl30 Chmp2a TBL1XR1 Sphkap Dnah1 Rpl31 Brix1 TBL1Y Styk1 Abca14 Rpl32 TCF7 Fastkd1 Cadps2 Tra2b Rmdn1 TCF7L1 Tbc1d30 Thsd7a Hmgb1 L7rn6 TCF7L2 Pde1c Arhgef37 Sumo1 Pycard TP53 Aga Ryr2 Rpl22 Rbp7 VANGL1 Insm1 Myof Ugt1a2 Nusap1 VANGL2 Arid3a Tns1 Rpl19 Hemgn WIF1 Tff3 Zfp945 Hist1h3b Ube3b WNT1 Sprr1a Mcf2l H3f3a Icoslg WNT10A Pea15 Dpysl3 Csrp2 Rangrf WNT10B Elavl4 9530053A07Rik Khk Pbk WNT11 Ktn1 Klc3 Rps3a Rpl38 WNT16 Ktn1 Pdia2 Myo7a Ap3b2 WNT2 Soat1 Fam46a Apoa1 Neu3 WNT2B Cfi Myo9a Bche Sult1b1 WNT3 Tmpo Bicd2 Rbp2 Fbp1 WNT3A Tmpo 2310045N01Rik Ssrp1 Slc5a1 WNT4 Lama5 Mgll Ces2f Adh4 WNT5A Ptprn Gm7849 Slc7a1 Suclg1 WNT5B Gm2a Gm15293 Prelid2 Pde3a WNT6 Lrrk2 Osbpl8 Pdss1 Mad2l1 WNT7A Pkdcc Bicd1 Dhrs11 Atp12a WNT7B C2cd4cC2CD4 Pls3 Slc16a10 Pck1 WNT8A Ang5 Arhgap4 Spc25 Rab4b WNT8B Gm14851 Vwa5b1 Wdr19 Gm12728 WNT9A Stxbp5l Glt1d1 Cks1brt Gm3550 WNT9B Galns Birc3 Capn13 Cluh Pnliprp2 Map1a Tbc1d9 Hepacam2 Bfsp1 Sez6l2 Cntln Trp53i11 Rap1gap Defa20 Frmpd1 Chn2 Npdc1 Heca Kiaa1324 Ampd1 Kiaa1324 Agt Sytl1 Zfp941 Ttc39a Peg3 Tbc1d16 Vwa5b2 Cdhr5 Pxdn Aspg

TABLE 3 Detected and quantified in vitro Proteome Table 3A. (FIG. 3B Proteome) M1-1 M1-2 M2-1 M2-2 Log2 Log2 Log2 Log2 Accession Median Median Median Median Average Gene Number Normalized Normalized Normalized Normalized logFC P.Value adj.P.Val change Symbol Entry Name Q9Z1S5 1.919 1.405 1.8885 1.833 1.833352 1.63E−06 0.000528463 up 42616 Neuronal-specific septin-3 Q9Z1B3 1.922 1.18 1.3575 2.007 1.616625 0.000542213 0.005190266 up Plcb1 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-1 Q9Z0Y2 3.79 3.377 3.9535 3.545 3.666375 9.91E−07 0.000496308 up Pla2g1b Phospholipase A2 Q9WVQ0 1.618 0.97 2.7755 1.716 1.713681 0.001071288 0.00723732 up Pmfbp1 Polyamine-modulated factor 1-binding protein 1 Q9WUA1 2.987 2.649 2.8515 2.698 2.796375 5.45E−07 0.000496308 up Wif1 Wnt inhibitory factor 1 Q9R013 2.399 2.243 2.1425 2.503 2.321875 1.62E−06 0.000528463 up Ctsf Cathepsin F Q9QXS6 1.932 1.914 2.2505 2.067 2.040875 2.28E−06 0.00058884 up Dbn1 Drebrin Q9JJV2 1.874 1.684 1.7955 1.925 1.819625 1.40E−06 0.000528463 up Pfn2 Profilin-2 Q9JJV1 2.127 1.298 2.4545 2.203 2.128054 1.87E−05 0.001261088 up Cryba2 Beta-crystallin A2 Q9JJN5 1.626 1.333 1.4785 2.041 1.619625 6.59E−05 0.002030382 up Cpn1 Carboxypeptidase N catalytic chain Q9EST1 2.424 2.069 2.3445 2.017 2.213625 5.70E−06 0.000861774 up Gsdma Gasdermin-A Q9ER67 1.351 1.54 1.7865 1.558 1.557372 7.50E−06 0.000936704 up Maged2 Maged2 protein Q9ER35 1.826 0.674 2.3155 2.445 1.829093 0.002378953 0.01135493 up Fn3k Fructosamine-3-kinase Q9DCB1 2.691 2.005 2.3475 1.98 2.255875 3.20E−05 0.00159398 up Hmgn3 High mobility group nucleosome-binding domain- containing protein 3 Q9D848 2.675 1.992 1.8715 0.311 1.873974 0.00120204 0.00774992 up AY761184 CRS1C-3 Q9D5R3 2.487 1.165 2.0435 1.588 1.820875 0.000920379 0.00671346 up Cep83 Centrosomal protein of 83 kDa Q9CWQ2 2.33 3.009 2.3595 3.382 2.770125 0.000103728 0.002461201 up Zswim7 Zinc finger SWIM domain-containing protein 7 Q9CR33 2.069 1.342 1.2615 2.246 1.729625 0.000986271 0.006963311 up Mansc1 MANSC domain-containing protein 1 Q9CQ89 2.206 1.342 1.5425 2.534 1.906125 0.000902097 0.006685812 up Cuta Protein CutA Q9CPX4 2.588 1.623 1.8175 2.291 2.079875 0.000190811 0.003192407 up Ftl1 Ferritin Q99N50-4 1.855 1.299 1.1175 1.8 1.517875 0.000437783 0.004711619 up Sytl2 Isoform 4 of Synaptotagmin-like protein 2 Q99JA5 2.204 2.403 2.0145 1.863 2.121125 9.16E−06 0.000991767 up Ly6e Ly6e protein Q921C5-2 2.114 1.381 1.7125 2.33 1.884375 0.000230276 0.003488521 up Bicd2 Isoform 2 of Protein bicaudal D homolog 2 Q91ZZ3 2.144 1.858 1.7555 1.529 1.821625 1.81E−05 0.001253109 up Sncb Beta-synuclein Q91XQ0 1.567 1.169 2.3695 2.239 1.836125 0.001115045 0.007397329 up Dnah8 Dynein heavy chain 8, axonemal Q91WD9 2.13 1.767 1.8935 2.339 2.032375 1.72E−05 0.001250999 up Scgn Secretagogin Q8R4S0 1.119 1.259 1.7095 1.989 1.519125 0.000576522 0.005337328 up Ppp1r14c Protein phosphatase 1 regulatory subunit 14C Q8R2S8 2.182 1.498 1.6015 1.344 1.600527 4.39E−05 0.001671268 up Cd177 CD177 antigen Q8R2K3 2.404 0.58 2.1815 2.104 2.1049 1.80E−05 0.001250999 up Ssbp1 Single-stranded DNA-binding protein Q8K3Z9 1.744 1.808 1.7995 1.892 1.8078 5.21E−07 0.000496308 up Pom121 Nuclear envelope pore membrane protein POM 121 Q8K0T2 1.792 1.765 1.7145 1.934 1.791711 8.47E−07 0.000496308 up Dync2li1 Cytoplasmic dynein 2 light intermediate chain 1 Q8K0D2 2.456 2.167 2.0875 1.888 2.149625 5.38E−06 0.00085901 up Habp2 Hyaluronan-binding protein 2 Q8CJ27 0.845 2.7 2.1305 2.806 2.133999 0.001979196 0.01017514 up Aspm Abnormal spindle-like microcephaly-associated protein homolog Q8CIN6-2 2.314 2.198 2.4995 2.371 2.345625 5.20E−07 0.000496308 up Celf3 Isoform 2 of CUGBP Elav-like family member 3 Q8CFE5 1.153 2.342 3.0785 3.406 2.494875 0.002199176 0.01077274 up Btbd7 BTB/POZ domain-containing protein 7 Q8CFC2-3 1.935 1.067 1.9645 1.796 1.79679 1.55E−05 0.001188215 up Myt1 Isoform 3 of Myelin transcription factor 1 Q8CEZ0 1.842 1.162 1.5555 1.768 1.581875 8.81E−05 0.0022847 up Kctd2 BTB/POZ domain-containing protein KCTD2 Q8C7E4 2.488 1.585 2.1965 2.083 2.088125 3.99E−05 0.001671268 up Rnase4 Ribonuclease 4 Q8C1N8 2.168 1.5 2.5205 1.437 1.906375 0.00069737 0.005839835 up Defa22 Alpha-defensin 22 Q8BY35 1.523 1.046 1.5595 1.542 1.523108 1.78E−06 0.000528463 up Fgd2 FYVE, RhoGEF and PH domain-containing protein 2 Q8BND5-3 2.129 0.898 1.4425 1.827 1.574125 0.001178576 0.00765406 up Qsox1 Isoform 3 of Sulfhydryl oxidase 1 Q810U3 1.119 1.431 2.5695 2.421 1.885125 0.003135872 0.0134757 up Nfasc Neurofascin Q80YQ1 3.024 2.945 3.0295 2.119 2.945374 2.32E−07 0.000496308 up Thbs1 Thrombospondin 1 Q80TJ1-2 1.972 1.265 1.8515 1.851 1.851242 1.31E−06 0.000528463 up Cadps Isoform 2 of Calcium-dependent secretion activator 1 Q6ZPF3 1.633 0.847 2.1345 2.305 1.729875 0.001781463 0.009562387 up Tiam2 T-lymphoma invasion and metastasis-inducing protein 2 Q6PDS3-3 1.743 0.951 2.2335 2.359 1.821625 0.001228506 0.007844821 up Sarm1 Isoform 3 of Sterile alpha and TIR motif-containing protein 1 Q6NSW3-3 1.756 1.428 1.6805 1.984 1.712125 1.50E−05 0.001188215 up Sphkap Isoform 3 of A-kinase anchor protein SPHKAP Q69ZT9 2.226 0.801 1.1895 2.285 1.625375 0.006727622 0.02192564 up Tbc1d30 TBC1 domain family member 30 Q64191 2.453 1.297 1.9965 2.404 2.037625 0.000306477 0.004006703 up Aga N(4)-(beta-N-acetylglucosaminyl)-L-asparaginase Q63ZV0 1.483 1.774 1.9485 2.364 1.892375 7.58E−05 0.002167266 up Insm1 Insulinoma-associated protein 1 Q61129 1.748 1.679 1.9225 1.619 1.742125 2.52E−06 0.000617538 up Cfi Complement factor I Q60648 1.975 1.26 2.0995 1.811 1.812253 5.30E−05 0.001844081 up Gm2a Ganglioside GM2 activator Q5S006 1.581 1.441 2.0715 1.555 1.580585 4.75E−06 0.000841369 up Lrrk2 Leucine-rich repeat serine/threonine-protein kinase 2 Q5GAN1 3.593 3.129 2.6745 1.695 2.772875 0.000461621 0.00480339 up Ang5 Angiogenin ribonuclease 5 Q5ERJ0 2.4 1.913 1.6085 1.019 1.735125 0.000908599 0.006696628 up Gm14851 CRS1C-2 Q4VBW7 2.049 1.436 0.9165 1.902 1.575875 0.001119831 0.0074168 up Pnliprp2 Pancreatic lipase-related protein 2 Q4V9Z5-2 1.801 1.432 1.5445 2.096 1.718375 6.72E−05 0.002044753 up Sez6l2 Isoform 2 of Seizure 6-like protein 2 Q45VN2 2.747 2.301 2.6535 2.726 2.653932 3.29E−07 0.000496308 up Defa20 Alpha-defensin 20 Q3V1N5 1.377 2.635 1.1905 2.006 1.802125 0.001896275 0.009962234 up Heca Protein Heca Q3URU2 1.824 1.533 1.6705 1.936 1.740875 8.73E−06 0.000977434 up Peg3 Paternally-expressed gene 3 protein Q3UP38 1.74 1.162 1.2965 1.802 1.500125 0.000259438 0.003686409 up Cracr2a EF-hand calcium-binding domain-containing protein 4B Q3UN27 2.666 2.04 2.1545 1.868 2.15338 1.41E−05 0.00118665 up Mmp7 Matrilysin Q3TTY0 2.343 1.775 1.8565 1.701 1.855881 5.14E−06 0.000841369 up Plb1 Phospholipase B1, membrane-associated Q3TMQ6 3.144 3.114 2.3885 2.14 2.696625 0.000127357 0.002612217 up Ang4 Angiogenin-4 Q32M21 2.749 1.938 2.5425 1.916 2.286375 0.000120733 0.002566457 up Gsdma2 Gasdermin-A2 Q08535 3.103 1.116 2.2905 2.843 2.338125 0.001432842 0.008537397 up Sct Secretin Q06890 1.554 2.165 1.5055 0.541 1.507456 0.00093134 0.00675869 up Clu Clusterin Q05421 1.95 2.17 1.5755 1.804 1.874875 1.79E−05 0.001250999 up Cyp2e1 Cytochrome P450 2E1 Q03517 1.625 1.264 1.2065 1.911 1.501625 0.000240264 0.003559107 up Scg2 Secretogranin-2 Q00896 3.029 0.896 1.7315 1.817 1.814205 0.001750144 0.009452505 up Serpina1c Alpha-1-antitrypsin 1-3 Q00493 1.892 1.749 1.3295 1.305 1.568875 0.000152612 0.002821684 up Cpe Carboxypeptidase E P97802 3.593 3.129 2.7415 1.826 2.822375 0.000283149 0.003852556 up Ang3 Angiogenin-3 P84086 2.11 2.087 1.7845 2.232 2.087446 1.05E−06 0.000496308 up Cplx2 Complexin-2 P80560 1.842 1.788 1.7775 2.039 1.841682 9.66E−07 0.000496308 up Ptprn2 Receptor-type tyrosine-protein phosphatase N2 P63239 2.186 1.731 1.7185 1.875 1.874158 8.06E−06 0.000936704 up Pcsk1 Neuroendocrine convertase 1 P59764 1.344 1.328 1.7175 2.399 1.697125 0.000509312 0.005029437 up Dock4 Dedicator of cytokinesis protein 4 P58283-3 1.708 1.374 1.9535 1.623 1.664625 2.09E−05 0.001321066 up Rnf216 Isoform 3 of E3 ubiquitin-protein ligase RNF216 P55200 1.21 0.543 2.2865 2.379 1.604625 0.01252816 0.03369151 up Kmt2a Histone-lysine N-methyltransferase 2A P55095 1.867 1.775 1.3065 1.679 1.679789 1.28E−05 0.00116258 up Gcg Glucagon P48437 1.7 2.102 2.1305 1.95 1.970625 5.57E−06 0.00085901 up Prox1 Prospero homeobox protein 1 P47877 3.024 2.897 2.9265 2.995 2.960625 5.40E−08 0.000432658 up Igfbp2 Insulin-like growth factor-binding protein 2 P47867 2.941 2.542 3.0155 2.834 2.834798 8.82E−07 0.000496308 up Scg3 Secretogranin-3 P46660 1.608 1.399 1.7475 1.64 1.608475 3.38E−06 0.000727205 up Ina Alpha-internexin P39654 1.401 0.766 1.7575 2.077 1.500375 0.001679611 0.009272174 up Alox15 Arachidonate 15-lipoxygenase P37889 1.671 1.018 2.3635 1.531 1.645875 0.00066484 0.00567162 up Fbln2 Fibulin-2 P35441 3.046 2.909 3.0575 2.156 2.909724 1.12E−06 0.000500631 up Thbs1 Thrombospondin-1 P28667 1.53 1.595 2.2025 1.74 1.739012 2.49E−05 0.001435728 up Marcksl1 MARCKS-related protein P28184 2.777 2.558 1.6965 1.512 2.135875 0.000981534 0.006958876 up Mt3 Metallothionein-3 P27577 2.244 1.471 2.0385 2.909 2.165625 0.000287722 0.003868799 up Ets1 Protein C-ets-1 P26339 2.449 2.137 2.6225 2.555 2.449782 1.72E−06 0.000528463 up Chga Chromogranin-A P22599 3.063 0.875 1.8055 2.069 1.953125 0.002738347 0.01237739 up Serpina1b Alpha-1-antitrypsin 1-2 P21570 2.195 1.555 1.7825 1.902 1.858625 2.06E−05 0.00131579 up Ang Angiogenin P21460 2.115 1.239 1.4025 1.775 1.632875 0.000321277 0.004048291 up Cst3 Cystatin-C P17897 2.927 1.667 2.2645 2.411 2.317375 0.000102461 0.00245844 up Lyz1 Lysozyme C-1 P17553 2.705 2.055 1.3575 1.691 1.952125 0.000563204 0.005287945 up Wnt3 Proto-oncogene Wnt-3 P16014 2.325 1.946 2.4405 2.366 2.325401 5.80E−07 0.000496308 up Chgb Secretogranin-1 P14873 2.39 2.04 2.3655 2.557 2.366088 1.03E−06 0.000496308 up Map1b Microtubule-associated protein 1B P14824 1.447 1.822 1.7405 1.364 1.593375 4.20E−05 0.001671268 up Anxa6 Annexin A6 P12961 1.893 1.303 1.4365 2.137 1.692375 0.000313666 0.00404438 up Scg5 Neuroendocrine protein 7B2 P12265 1.978 0.304 2.2855 1.948 1.948861 2.40E−05 0.001402557 up Gusb Beta-glucuronidase P11276 1.8 1.665 1.5365 1.802 1.700875 3.45E−06 0.000727205 up Fn1 Fibronectin P10107 1.937 2.608 2.6415 1.284 2.117625 0.00082677 0.006357335 up Anxa1 Annexin A1 P09240 2.26 0.481 1.4655 2.002 1.552125 0.005770574 0.01983078 up Cck Cholecystokinin P08553 1.584 1.357 1.5325 1.646 1.532958 3.63E−06 0.000728919 up Nefm Neurofilament medium polypeptide P08551 1.697 1.481 1.6825 1.788 1.682822 1.55E−06 0.000528463 up Nefl Neurofilament light polypeptide P08228 1.826 0.892 1.1695 2.321 1.552125 0.003743497 0.01523324 up Sod1 Superoxide dismutase [Cu—Zn] P06797 2.377 0.802 2.2995 1.808 1.821625 0.001780753 0.009562387 up Ctsl Cathepsin L1 P00683 2.99 2.203 2.7165 4.381 2.987052 0.000227931 0.003478735 up Rnase1 Ribonuclease pancreatic O88312 2.309 1.237 0.9115 1.981 1.609625 0.003576391 0.01478143 up Agr2 Anterior gradient protein 2 homolog O35684 1.863 1.077 1.8075 1.545 1.573125 0.000179541 0.003114218 up Serpini1 Neuroserpin O08599 1.813 1.126 1.5275 1.761 1.556875 0.000108367 0.002481296 up Stxbp1 Syntaxin-binding protein 1 F8VQA4 1.721 1.405 1.5215 2.077 1.681125 5.94E−05 0.001942086 up Pam Peptidyl-glycine alpha-amidating monooxygenase F6V035 1.704 1.098 1.5555 1.608 1.55601882 7.78E−06 0.000936704 up Ccdc149 Protein Ccdc149 E9Q8F8 2.503 0.663 3.0695 3.976 2.552875 0.006045857 0.020426433 up Abca14 Protein Abca14 E9Q835 1.838 1.662 2.1005 1.977 1.894375 6.57E−06 0.000907306 up Cadps2 Calcium-dependent secretion activator 2 E9Q6P0 2.347 1.477 2.0985 1.766 1.922125 0.000124875 0.002592615 up Thsd7a Thrombospondin type-1 domain-containing protein 7A E9Q0S6 0.944 1.445 2.2135 2.088 1.672625 0.001864277 0.009855092 up Tns1 Protein Tns1 E9PYM8 2.176 0.688 1.6965 2.47 1.757625 0.003075388 0.01332225 up Zfp945 Protein Zfp945 D3Z6P0 2.132 1.103 1.3525 2.061 1.662125 0.001263763 0.007993525 up Pdia2 Protein disulfide-isomerase A2 D3Z390 2.48 1.385 1.8445 2.432 2.035375 0.000428866 0.004669744 up Bicd2 Bicaudal D homolog 2 (Drosophila ), isoform CRA_a D3Z373 2.955 2.218 2.5985 1.87 2.410375 0.000102173 0.00245844 up 2310045N01Rik Protein 2310045N01Rik D3YYS6 1.648 1.052 2.1255 1.654 1.649334666 0.000111604 0.002493535 up Mgll Monoglyceride lipase D3YX03 2.165 2.033 1.8715 0.909 1.872684813 5.84E−05 0.001932826 up Gm7849 Protein Gm7849 B1AUY3 1.818 1.365 2.2695 2.992 2.111125 0.000935093 0.006763392 up Arhgap4 Protein Arhgap4 A9Z1V5 1.539 1.688 1.5255 2.014 1.68713745 1.56E−05 0.001188215 up Vwa5b1 von Willebrand factor A domain-containing protein 5B1 A2ARP8 1.921 1.711 1.3865 1.08 1.524625 0.000329271 0.004078484 up Map1a Microtubule-associated protein 1A A2AMT1 1.593 0.651 2.1025 3.084 1.857625 0.007265371 0.023206332 up Bfsp1 Filensin A2AJ21 2.322 1.851 2.3395 2.486 2.322461069 8.46E−07 0.000496308 up Npdc1 Neural proliferation differentiation and control protein 1 A0JNU3 2.302 1.857 3.2165 3.898 2.818375 0.001208178 0.007770736 up Aspg 60 kDa lysophospholipase A2ACP1 1.442 1.172 1.1125 0.996 1.171348084 3.75E−05 0.001639477 up Ttc39a Tetratricopeptide repeat protein 39A A2AFS3 1.738 1.764 1.1595 1.209 1.467625 0.000349563 0.004189781 up Kiaa1324 UPF0577 protein KIAA1324 A2AFS3-2 1.681 1.724 1.0495 1.089 1.385875 0.000737371 0.00598712 up Kiaa1324 Isoform 2 of UPF0577 protein KIAA1324 A2AHJ4 −1.325 −1.312 −1.6885 −1.8 −1.531375 8.48E−05 0.002275515 down Brwd3 Bromodomain and WD repeat-containing protein 3 A2ALS5-3 1.428 1.017 1.1795 1.271 1.223875 3.48E−05 0.001614723 up Rap1gap Isoform 3 of Rap1 GTPase-activating protein 1 A2AM05 0.712 1.749 0.9975 2.238 1.424125 0.007701384 0.024193998 up Cntin Centlein A2APM2 −1.843 −1.042 −1.9235 −2.326 −1.844546108 0.00013512 0.002680332 down Cd44 CD44 antigen A2AR02 −1.642 −0.589 −0.8735 −1.422 −1.131625 0.004865676 0.017961089 down Ppig Peptidyl-prolyl cis-trans isomerase G A2ARV4 −1.422 0.033 −1.2255 −1.188 −1.188635091 8.70E−05 0.0022847 down Lrp2 Low-density lipoprotein receptor-related protein 2 A2CGA5 0.6 1.467 1.1335 1.508 1.177125 0.001431007 0.008532994 up Birc3 Baculoviral IAP repeat-containing protein 3 B1AR10 −1.932 −0.948 −2.3265 −3.084 −2.072625 0.002417885 0.011458858 down Mllt6 Protein Mllt6 B1ARD6 −1.624 −0.756 −0.8195 −1.569 −1.192125 0.004058816 0.016007553 down Slfn9 Protein Slfn9 B1ASD8 −1.151 −0.693 −0.6625 −2.146 −1.148345484 0.008969669 0.026852047 down Gm13251 Protein Gm13251 B1AVH5 −1.404 −1.422 −1.7495 −1.134 −1.421153941 3.43E−05 0.001614723 down Coro2a Coronin B1AX39 −1.151 −2.339 −1.3705 −1.88 −1.685125 0.001071961 0.00723732 down Zcchc7 Zinc finger CCHC domain-containing protein 7 B1B1D3 −1.69 −0.307 −1.2965 −2.86 −1.538375 0.015394521 0.038918513 down Zfp40 Protein Zfp40 B2KG46 1.226 1.158 1.4615 1.248 1.247704648 6.46E−06 0.000907306 up Bicd1 Protein bicaudal D homolog 1 B2RU80 −1.888 −1.404 −2.2815 −2.537 −2.027625 0.000281594 0.00384147 down Ptprb Receptor-type tyrosine-protein phosphatase beta B9EJ86 1.242 1.864 1.0905 0.802 1.240341508 0.000930338 0.00675869 up Osbpl8 Oxysterol-binding protein B9EJA2 −1.439 −1.031 −0.9535 −1.2 −1.155875 0.000116764 0.00252203 down Cttnbp2 Cortactin-binding protein 2 D3YU60 −1.514 −0.88 −2.0875 −0.38 −1.215375 0.015984588 0.03996895 down Mgst1 Microsomal glutathione S-transferase 1 D3YUE4 −0.678 −1.053 −1.3175 −1.611 −1.164875 0.001290203 0.008102551 down Fam151b Protein Fam151b D3YX02 1.354 1.275 1.1975 1.386 1.303125 5.09E−06 0.000841369 up Gm15293 Protein Gm15293 D3YX71 −0.602 −2.402 −1.3475 −3.186 −1.884375 0.015728602 0.039526188 down Gm8973 Uncharacterized protein D3YYD0 −2.58 −1.045 1.8875 −1.993 −1.889730404 0.000485724 0.004937744 down Olfm4 Olfactomedin-4 D3Z3A8 1.271 2.016 1.5115 0.837 1.408875 0.001116807 0.007402891 up Myo9a Unconventional myosin-IXa D3Z4T9 −1.692 −1.338 −1.4265 −2.701 −1.690333075 0.000329135 0.004078484 down Zranb2 Zinc finger Ran-binding domain-containing protein 2 D3Z710 1.511 1.04 1.3825 1.574 1.383384734 4.61E−05 0.001710782 up Klc3 Kinesin light chain 3 E0CX20 −2.039 −1.624 −2.3525 −2.74 −2.188875 0.00014518 0.002763462 down Bud31 Protein BUD31 homolog E9PUQ3 −1.916 −1.183 −1.5635 −2.66 −1.830625 0.00102024 0.007094039 down AU019823 Protein AU019823 E9PV38 −1.433 −1.225 −1.5595 −1.408 −1.408493743 6.38E−06 0.000907306 down Ces2g Protein Ces2g E9PXE2 1.372 1.007 1.2045 1.385 1.242125 4.27E−05 0.001671268 up Mcf2l Guanine nucleotide exchange factor DBS E9PY03 −1.832 −1.927 −1.9725 −1.438 −1.83263141 4.97E−06 0.000841369 down Tstd1 Upstream stimulatory factor 1 E9Q1Q9 −1.228 −2.256 −1.4795 −0.174 −1.284375 0.012772242 0.034187291 down Khk Ketohexokinase E9Q390 1.279 1.429 0.8835 0.99 1.145375 0.000314204 0.00404438 up Myof Myoferlin E9Q409 −1.155 −0.943 −1.4935 −1.12 −1.154318401 5.14E−05 0.001809458 down Prss32 Protein Prss32 E9Q5C9 −1.968 −1.821 −1.5075 −2.239 −1.883875 3.52E−05 0.001614723 down Nolc1 Protein Nolc1 E9Q5K9 −1.951 −1.083 −1.7955 −2.091 −1.796718589 6.16E−05 0.001952061 down Ythdc1 YTH domain-containing protein 1 E9Q5R6 1.186 0.722 1.7735 0.904 1.146375 0.002170846 0.010666562 up Arhgef37 Rho guanine nucleotide exchange factor 37 E9Q8N8 −1.359 −0.987 −1.7165 −2.079 −1.535375 0.000823844 0.006357335 down Slc4a4 Electrogenic sodium bicarbonate cotransporter 1 E9Q9C6 1.523 0.778 0.9895 1.436 1.181625 0.001183899 0.007660319 up Fcgbp Protein Fcgbp E9QLR9 −2.131 −2.144 −1.7675 −2.046 −2.046497064 1.34E−06 0.000528463 down Ddias DNA damage-induced apoptosis suppressor protein E9QNS0 −1.517 −1.262 −1.3005 −1.178 −1.300054355 8.78E−06 0.000977434 down Nlrp6 NACHT, LRR and PYD domains-containing protein 6 E9QNX7 −1.411 −0.605 −2.7825 −2.921 −1.929875 0.015107954 0.038448758 down Atp4a Potassium-transporting ATPase alpha chain 1 F2Z423 −1.459 −0.535 −2.0165 −0.743 −1.188375 0.013748101 0.03598213 down Ttll12 Tubulin-tyrosine ligase-like protein 12 F6R4Z5 −1.473 −0.647 −1.1325 −1.652 −1.226125 0.001668908 0.009264408 down Zfp709 Protein Zfp709 F6V243 0.958 0.871 1.1595 1.86 1.158156729 0.0006775 0.005715245 up Pcdhb12 Protein Pcdhb12 F8VQC7 1.447 1.452 1.2755 1.397 1.397289615 2.70E−06 0.000617538 up Ktnl Kinectin F8WIA4 1.349 0.712 1.3545 1.411 1.349125974 3.64E−06 0.000728919 up Sgsm3 Small G protein-signaling modulator 3 G3X8T2 −1.171 −1.171 −0.7325 −1.289 −1.170987 1.16E−05 0.001090211 down Zc3h18 RIKEN cDNA 5830416A07, isoform CRA_c G3X956 −1.701 −0.681 −1.0595 −1.804 −1.311375 0.003855666 0.0155351 down Supt16 FACT complex subunit SPT16 G3X9H7 1.27 1.333 1.3185 1.878 1.332838 4.14E−06 0.000790475 up Mtss1 Metastasis suppressor 1, isoform CRA_e G5E904 −1.362 −1.619 −2.9455 −2.181 −2.026875 0.001296975 0.008106338 down Gm4794 Sulfotransferase I1E4X8 1.149 1.163 1.4315 1.271 1.253625 1.45E−05 0.00118665 up Stim2 Stromal interaction molecule 2 J3QMG3 −0.916 −0.797 −1.4855 −1.663 −1.215375 0.002277135 0.0110199 down Vdac3 Voltage-dependent anion-selective channel protein 3 K3W4L7 −1.188 −1.811 −1.9375 −0.883 −1.454875 0.001977855 0.01017514 down Pbld1 Phenazine biosynthesis-like domain-containing protein 1 O08529 1.421 1.297 1.1725 1.347 1.309375 6.15E−06 0.000907306 up Capn2 Calpain-2 catalytic subunit O09010 1.443 1.37 1.4835 1.56 1.464125 2.24E−06 0.00058884 up Lfng Beta-1,3-N-acetylglucosaminyltransferase lunatic fringe O09037 −1.64 −2.141 −1.5875 −1.077 −1.611375 0.000210039 0.00333318 down Reg3a Regenerating islet-derived protein 3-alpha O35280 −1.09 −1.001 −1.4995 −1.475 −1.266375 0.000245954 0.003578677 down Chek1 Serine/threonine-protein kinase Chk1 O35594 0.817 1.152 1.1275 1.543 1.150998 0.000176264 0.003085355 up Ift81 Intraflagellar transport protein 81 homolog O35943 −0.813 −0.849 −1.3945 −1.715 −1.192875 0.002560222 0.01190766 down Fxn Frataxin, mitochondrial O35945 −1.241 −1.721 −1.8345 −0.518 −1.328625 0.003926343 0.01565951 down Aldh1a7 Aldehyde dehydrogenase, cytosolic 1 O54864-2 −1.557 −1.413 −1.3965 −2.183 −1.556204 2.90E−05 0.001546817 down Suv39h1 Isoform 2 of Histone-lysine N-methyltransferase SUV39H1 O55042 1.666 1.165 1.2265 1.268 1.267636 1.03E−05 0.001045334 up Snca Alpha-synuclein O70126 −1.572 −0.967 −0.8395 −1.281 −1.164875 0.000734879 0.005979009 down Aurkb Aurora kinase B O70472 1.419 0.87 1.3875 1.011 1.171875 0.000429715 0.004672636 up Tmem131 Transmembrane protein 131 O70514 −1.413 −1.091 −1.0895 −1.216 −1.202375 2.65E−05 0.001486938 down Fgfbp1 Fibroblast growth factor-binding protein 1 O88310 1.445 1.239 0.9545 1.175 1.203375 5.28E−05 0.001844081 up Itln1 Intelectin-1a O88451 −1.202 −1.565 −2.2355 −0.662 −1.416125 0.004075268 0.01602497 down Rdh7 Retinol dehydrogenase 7 O88513 −1.6 −1.306 −0.8435 −1.599 −1.337125 0.00039035 0.004430968 down Gmnn Geminin O88554 −1.403 −0.933 −1.4925 −1.465 −1.403376 7.08E−06 0.000936704 down Parp2 Poly [ADP-ribose] polymerase 2 O88803 1.692 1.063 1.4425 1.463 1.443242 2.35E−05 0.001402557 up Lect2 Leukocyte cell-derived chemotaxin-2 P02772 −1.616 −1.696 −1.1235 −1.316 −1.437875 0.000127121 0.002612217 down Afp Alpha-fetoprotein P02798 −2.904 −2.907 −2.2505 −3.047 −2.904342 1.91E−07 0.000496308 down Mt2 Metallothionein-2 P02802 −2.19 −2.322 −1.3715 −1.016 −1.724875 0.002557451 0.01190766 down Mt1 Metallothionein-1 P03958 1.339 0.074 1.5985 1.501 1.340051 0.000235506 0.003521621 up Ada Adenosine deaminase P04184 −1.268 −1.033 −1.0175 −1.428 −1.186625 9.77E−05 0.002401232 down Tk1 Thymidine kinase, cytosolic P06728 −1.343 −2.171 −1.8605 −0.907 −1.570375 0.001819873 0.00967781 down Apoa4 Apolipoprotein A-IV P07309 1.309 0.951 1.2255 1.511 1.249125 7.53E−05 0.002163145 up Ttr Transthyretin P07310 −1.418 −3.14 −2.0165 −2.541 −2.278875 0.000931913 0.00675869 down Ckm Creatine kinase M-type P09405 −1.377 −0.807 −1.0695 −1.615 −1.217125 0.000783546 0.006190813 down Ncl Nucleolin P0C027 1.368 1.133 0.8135 1.192 1.133819 8.97E−05 0.002304862 up Nudt10 Diphosphoinositol polyphosphate phosphohydrolase 3- alpha P11725 −1.478 −1.458 −2.2695 −1.132 −1.477049 7.65E−05 0.002167266 down Otc Ornithine carbamoyltransferase, mitochondrial P14115 −1.536 −1.734 −0.8425 −2.121 −1.558375 0.000833707 0.006381402 down Rpl27a 60S ribosomal protein L27a P18242 1.508 1.211 0.9875 1.479 1.296375 0.000138492 0.002700428 up Ctsd Cathepsin D P18581-2 −1.863 −1.174 −2.2475 −3.161 −2.111375 0.001677287 0.009272174 down Slc7a2 Isoform 2 of Low affinity cationic amino acid transporter 2 P18894 −1.222 −1.706 −1.8305 −0.745 −1.375875 0.001910795 0.009965945 down Dao D-amino-acid oxidase P19246 1.432 1.357 1.1695 1.176 1.283625 1.86E−05 0.001261088 up Nefh Neurofilament heavy polypeptide P19467 1.437 0.978 1.3955 0.984 1.198625 0.000300581 0.003962314 up Muc13 Mucin-13 P23881 −1.331 −1.172 −1.7775 −1.12 −1.329973 0.000104034 0.002461201 down Tcea3 Transcription elongation factor A protein 3 P25444 −1.207 −1.264 −1.1365 −2.462 −1.263604 2.14E−05 0.001337621 down Rps2 40S ribosomal protein S2 P27600 −1.957 −1.145 −2.8495 −2.827 −2.194625 0.002022413 0.01030991 down Gna12 Guanine nucleotide-binding protein subunit alpha-12 P27659 −1.484 −1.144 −0.9115 −1.972 −1.377875 0.001166624 0.007619665 down Rpl3 60S ribosomal protein L3 P28650-2 −1.408 −0.831 −1.4375 −1.789 −1.409128 0.000128476 0.002612217 down Adssl1 Isoform 2 of Adenylosuccinate synthetase isozyme 1 P30681 −1.316 −1.094 −1.2715 −1.62 −1.315261 3.18E−05 0.00159398 down Hmgb2 High mobility group protein B2 P31362 −1.567 −1.082 −2.3845 −2.554 −1.896875 0.002319706 0.01115185 down Pou2f3 POU domain, class 2, transcription factor 3 P40338 −1.026 −1.492 −1.5695 −2.043 −1.532625 0.000244704 0.003578573 down Vhl Von Hippel-Lindau disease tumor suppressor P43137 −2.092 −3.168 −4.1035 −2.045 −2.852125 0.001489254 0.008686232 down Reg1 Lithostathine-1 P43883 1.328 1.122 0.9365 1.559 1.236375 0.000212153 0.003357025 up Plin2 Perilipin-2 P47968 −0.958 −1.223 −1.2935 −1.827 −1.292372 0.000180309 0.003114218 down Rpia Ribose-5-phosphate isomerase P48036 1.196 1.332 1.1055 0.94 1.143375 4.26E−05 0.001671268 up Anxa5 Annexin A5 P48281 −1.589 −1.441 −1.0795 −1.499 −1.441549 1.11E−05 0.001083377 down Vdr Vitamin D3 receptor P48756 1.21 0.504 1.2845 1.769 1.211741 0.001425305 0.00852239 up Gip Gastric inhibitory polypeptide P50431 −1.382 −1 −1.1875 −1.08 −1.162375 4.12E−05 0.001671268 down Shmt1 Serine hydroxymethyltransferase, cytosolic P50543 1.371 1.475 1.4645 0.855 1.371501 1.44E−05 0.00118665 up S100a11 Protein S100-A11 P51162 −0.519 −1.799 −2.7635 −1.209 −1.572625 0.01221016 0.03311413 down Fabp6 Gastrotropin P51432 −1.261 −1.255 −1.1345 −1.096 −1.186625 9.15E−06 0.000991767 down Plcb3 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3 P52792 1.847 0.711 1.3025 0.805 1.166375 0.004637109 0.01733293 up Gck Glucokinase P52800 −0.883 −1.258 −1.7545 −1.065 −1.240125 0.000589978 0.005397356 down Efnb2 Ephrin-B2 P55050 −1.558 −2.656 −2.1955 −0.474 −1.720875 0.008358524 0.02568169 down Fabp2 Fatty acid-binding protein, intestinal P55088-3 −2.495 −1.955 −2.0905 −3.021 −2.390375 0.000108035 0.002481296 down Aqp4 Isoform 3 of Aquaporin-4 P56382 −1.051 −3.179 −1.3955 −3.924 −2.387375 0.01622922 0.04041672 down Atp5e ATP synthase subunit epsilon, mitochondrial P56395 −1.162 −0.964 −1.6925 −1.71 −1.382125 0.000772361 0.006143504 down Cyb5a Cytochrome b5 P56695 1.527 0.901 0.7335 1.433 1.148625 0.002098924 0.01049665 up Wfs1 Wolframin P56716 0.494 1.733 1.3015 1.329 1.302723 0.00032442 0.004068699 up Rp1 Oxygen-regulated protein 1 P60824 0.902 1.138 1.3145 1.267 1.155375 5.93E−05 0.001942086 up Cirbp Cold-inducible RNA-binding protein P61358 −1.508 −0.773 −1.0115 −2.267 −1.389875 0.004942579 0.01806194 down Rpl27 60S ribosomal protein L27 P61514 −1.096 −1.38 −0.8275 −1.528 −1.207875 0.000481327 0.004920094 down Rpl37a 60S ribosomal protein L37a P61961 1.579 0.388 1.1535 1.335 1.155166 0.001572259 0.008987222 up Ufm1 Ubiquitin-fold modifier 1 P62082 −1.274 −0.974 −1.0365 −1.419 −1.175875 0.000125912 0.002607376 down Rps7 40S ribosomal protein S7 P62245 −1.248 −1.487 −1.6535 −2.486 −1.651936 0.000247161 0.003581352 down Rps15a 40S ribosomal protein S15a P62267 −0.983 −2.038 −0.8085 −2.125 −1.488625 0.007553257 0.0238341 down Rps23 40S ribosomal protein S23 P62270 −1.433 −1.873 −1.1505 −1.958 −1.603625 0.000348729 0.004189781 down Rps18 40S ribosomal protein S18 P62806 −1.39 −0.628 −1.3305 −1.477 −1.331005 2.00E−05 0.001303913 down Hist1h4a Histone H4 P62830 −1.36 −1.128 −1.1215 −1.476 −1.271375 4.92E−05 0.001760748 down Rpl23 60S ribosomal protein L23 P62852 −2.56 −2.842 −2.8515 −4.104 −2.850786 1.68E−06 0.000528463 down Rps25 40S ribosomal protein S25 P62855 −1.566 −1.344 −1.0195 −2.026 −1.488875 0.000462717 0.00480339 down Rps26 40S ribosomal protein S26 P62876 −1.008 −0.747 −1.2095 −1.636 −1.150125 0.000925224 0.006740675 down Polr2l DNA-directed RNA polymerases I, II, and III subunit RPABC5 P62889 −1.84 −0.669 −1.4315 −2.06 −1.500125 0.002329107 0.01117023 down Rpl30 60S ribosomal protein L30 P62900 −1.746 −1.364 −1.5065 −2.581 −1.744279 0.000264424 0.003717712 down Rpl31 60S ribosomal protein L31 P62911 −1.244 −0.959 −0.6925 −1.954 −1.212375 0.003137717 0.0134757 down Rpl32 60S ribosomal protein L32 P63158 −1.875 −1.062 −1.2145 −1.339 −1.337887 0.000147143 0.002781147 down Hmgb1 High mobility group protein B1 P63166 −1.207 −1.094 −1.7425 −1.532 −1.393875 0.000233255 0.003516544 down Sumo1 Small ubiquitin-related modifier 1 P67984 −1.504 −1.157 −1.4345 −1.242 −1.334375 2.90E−05 0.001546817 down Rpl22 60S ribosomal protein L22 P70429 1.275 1.519 1.2085 1.206 1.27464 7.74E−06 0.000936704 up Evl Ena/VASP-like protein P81117 1.736 1.385 1.0905 1.276 1.371875 8.84E−05 0.0022847 up Nucb2 Nucleobindin-2 P84099 −1.093 −0.396 −1.3905 −3.354 −1.38699 0.01628257 0.04051181 down Rpl19 60S ribosomal protein L19 P84102 1.517 0.63 2.2205 0.775 1.285625 0.01270342 0.03404856 up Serf2 Small EDRK-rich factor 2 P84228 −1.226 −0.594 −1.0075 −1.809 −1.159125 0.002789439 0.01251655 down Hist1h3b Histone H3.2 P84244 −1.002 −0.645 −1.1735 −1.765 −1.146375 0.001900587 0.00996347 down H3f3a Histone H3.3 P97290 1.362 1.123 1.2185 1.278 1.245375 7.88E−06 0.000936704 up Serping1 Plasma protease C1 inhibitor P97314 −1.447 −1.021 −1.3045 −1.045 −1.204375 0.000114077 0.002510641 down Csrp2 Cysteine and glycine-rich protein 2 P97328 −1.151 −2.263 −1.4115 −0.12 −1.236375 0.01650177 0.0408795 down Khk Ketohexokinase P97351 −1.36 −0.944 −1.2445 −1.603 −1.287875 0.000133059 0.00265106 down Rps3a 40S ribosomal protein S3a P97449 1.246 1.528 1.2875 0.807 1.246894 9.00E−05 0.002304862 up Anpep Aminopeptidase N P97479 −1.135 −1.101 −1.2195 −1.191 −1.161625 5.01E−06 0.000841369 down Myo7a Unconventional myosin-VIIa P98063 1.296 1.342 1.2215 1.383 1.310625 3.35E−06 0.000727205 up Bmp1 Bone morphogenetic protein 1 Q00623 −1.311 −2.229 −2.6175 −1.952 −2.027375 0.000332404 0.004091988 down Apoa1 Apolipoprotein A-I Q03157 1.177 0.671 1.2695 1.559 1.178316 0.000473947 0.004869505 up Aplp1 Amyloid-like protein 1 Q03172 0.832 1.656 1.2325 1.102 1.205625 0.000427038 0.004665286 up Hivep1 Zinc finger protein 40 Q03311 −1.349 −1.892 −2.0655 −1.665 −1.742875 6.97E−05 0.002060325 down Bche Cholinesterase Q05186 1.602 1.092 1.0235 1.511 1.307125 0.000350601 0.004189781 up Rcn1 Reticulocalbin-1 Q07797 1.212 1.255 1.1065 1.011 1.146125 1.69E−05 0.001250999 up Lgals3bp Galectin-3-binding protein Q08652 −1.364 −2.41 −1.7785 −0.366 −1.479625 0.008932341 0.02676029 down Rbp2 Retinol-binding protein 2 Q08943-2 −2.098 −0.891 −1.6565 −2.418 −1.765875 0.001656867 0.009240863 down Ssrp1 Isoform 2 of FACT complex subunit SSRP1 Q08ED5 −1.702 −1.686 −2.2885 −1.679 −1.701948 9.51E−07 0.000496308 down Ces2f Protein Ces2f Q2QI47-3 1.068 0.864 1.5445 2.117 1.398375 0.002682728 0.01228429 up Ush2A Isoform 3 of Usherin Q32NZ6 1.76 1.111 1.2165 1.252 1.251557 1.73E−05 0.001250999 up Tmc5 Transmembrane channel-like protein 5 Q33DR2 −1.379 −1.779 −1.2185 −1.389 −1.388531 1.01E−05 0.001045334 down Pdss1 Decaprenyl-diphosphate synthase subunit 1 Q3TMX5 1.514 0.958 1.0245 1.141 1.140175 0.000100387 0.002445284 up Manf Arginine-rich, mutated in early stage tumors, isoform CRA_b Q3U0B3 −1.054 −1.691 −1.5305 −0.923 −1.299625 0.000920288 0.00671346 down Dhrs11 Dehydrogenase/reductase SDR family member 11 Q3U9N9 −1.309 −0.055 −1.4695 −2.424 −1.314375 0.01582461 0.03968035 down Slc16a10 Monocarboxylate transporter 10 Q3UA16 −1.924 −0.747 −1.8235 −2.598 −1.825917 0.000929435 0.00675869 down Spc25 Kinetochore protein Spc25 Q3UGF1 −0.199 −0.895 −1.3115 −2.206 −1.152875 0.0220145 0.04990783 down Wdr19 WD repeat-containing protein 19 Q3UHD3 1.347 0.087 1.7985 2.649 1.470375 0.01980273 0.04649841 up Mtus2 Microtubule-associated tumor suppressor candidate 2 homolog Q3UQ28 1.157 1.486 1.3875 1.146 1.294125 4.09E−05 0.001671268 up Pxdn Peroxidasin homolog Q3UR50 1.678 1.171 1.6125 1.377 1.459625 6.14E−05 0.001952061 up Vwa5b2 von Willebrand factor A domain-containing protein 5B2 Q3UTR7 1.922 1.275 0.9175 1.671 1.446375 0.00093424 0.006763325 up Agt Angiotensinogen Q3UW68 −1.402 −1.492 −1.0855 −0.676 −1.163875 0.001025725 0.007094039 down Capn13 Calpain-13 Q3UYK3 −0.639 −1.148 −1.5035 −1.709 −1.249875 0.001952687 0.01011701 down Tbc1d9 TBC1 domain family member 9 Q3V1V3 −1.45 −0.805 −0.9155 −1.805 −1.243875 0.002715757 0.01232664 down Esf1 ESF1 homolog Q3V2R3 1.307 0.981 1.2265 1.433 1.236875 4.02E−05 0.001671268 up Chn2 Beta-chimaerin Q3V3I2 −1.715 −1.092 −2.2685 −2.719 −1.948625 0.001663852 0.009259797 down Gnat3 Guanine nucleotide-binding protein G(t) subunit alpha-3 Q4ACU6 −1.525 −1.512 −1.6745 −1.835 −1.636625 6.84E−06 0.000929123 down Shank3 SH3 and multiple ankyrin repeat domains protein 3 Q4V9W2 −1.902 −0.824 −1.2515 −1.464 −1.360375 0.000870895 0.006534741 down Srek1ip1 Protein SREK1IP1 Q4VAH7 1.047 1.639 1.2475 1.739 1.418125 0.000338703 0.004128361 up Hepacam 2 HEPACAM family member 2 Q52KI8 −1.036 −0.819 −1.2825 −1.437 −1.143625 0.000364985 0.004285573 down Srrm1 Serine/arginine repetitive matrix protein 1 Q52KR3 −2.118 −0.268 −1.3905 −1.67 −1.393319 0.005328674 0.01891231 down Prune2 Protein prune homolog 2 Q571E4 1.473 0.565 1.3465 1.206 1.207102 0.000274726 0.003776421 up Galns N-acetylgalactosamine-6-sulfatase Q5DQR4 1.316 0.966 1.1715 1.133 1.146625 2.22E−05 0.001378179 up Stxbp5l Syntaxin-binding protein 5-like Q5HZI2 0.822 0.518 1.5305 1.762 1.158125 0.009692916 0.02823665 up C2cd4cC2CD4 C2 calcium-dependent domain-containing protein 4C Q60604 −1.236 −2.062 −1.8295 −0.073 −1.300125 0.01779587 0.04310892 down Scin Adseverin Q60673 1.189 1.249 0.8005 1.265 1.189341 1.27E−05 0.00116258 up Ptprn Receptor-type tyrosine-protein phosphatase-like N Q60936 −1.293 −1.012 −1.8255 −1.133 −1.291776 0.000242562 0.003568078 down Adck3 Chaperone activity of bc1 complex-like, mitochondrial Q60936-2 −1.293 −0.997 −1.7905 −1.133 −1.291732 0.000263845 0.00371608 down Adck3 Isoform 2 of Chaperone activity of bc1 complex-like, mitochondrial Q60997 −1.643 −0.987 −1.1555 −1.543 −1.332125 0.000387772 0.004425905 down Dmbt1 Deleted in malignant brain tumors 1 protein Q61263 1.563 2.15 1.0245 0.494 1.307875 0.009386066 0.02771552 up Soat1 Sterol O-acyltransferase 1 Q61391 −0.83 −1.694 1.3345 −0.675 −1.133375 0.003947765 0.01569426 down Mme Neprilysin Q61595- 1.391 1.442 1.2765 1.384 1.384175 2.17E−06 0.00058884 up Ktn1 Isoform 11 of Kinectin Q61595-5 1.485 1.462 1.2985 1.415 1.415329 2.70E−06 0.000617538 up Ktn1 Isoform 5 of Kinectin Q62395 1.037 1.294 0.4235 1.984 1.184625 0.006673775 0.02177672 up Tff3 Trefoil factor 3 Q62431 1.672 1.343 1.2465 0.741 1.250625 0.000488858 0.004942706 up Arid3a AT-rich interactive domain-containing protein 3A Q64176 −1.21 −1.557 −1.2065 −1.062 −1.209609 1.36E−05 0.001175119 down Ces1e Carboxylesterase 1E Q642K5 −1.384 −1.443 −1.4375 −2.406 −1.442913 2.62E−06 0.000617538 down Fau 40S ribosomal protein S30 Q64338 0.73 0.722 1.3705 1.805 1.156875 0.00595713 0.02020332 up Pde1c Calcium/calmodulin-dependent 3′,5′-cyclic nucleotide phosphodiesterase 1C Q64669 −1.603 −2.001 −1.5715 −0.844 −1.572746 0.000128653 0.002612217 down Nqo1 NAD(P)H dehydrogenase [quinone] 1 Q6DI86 1.46 1.066 1.4225 2.251 1.458857 0.000148835 0.002806503 up Fastkd1 FAST kinase domain-containing protein 1 Q6J9G1 1.631 1.194 0.7015 1.233 1.195311 0.000441484 0.004730011 up Styk1 Tyrosine-protein kinase STYK1 Q6PCN3 0.917 1.005 1.5695 1.711 1.300625 0.00133176 0.00822244 up Ttbk1 Tau-tubulin kinase 1 Q6PDB7 −0.858 −1.424 −1.6495 −1.282 −1.303375 0.00026931 0.003740468 down Ces2b MCG142671, isoform CRA_b Q6PEP4 −1.629 −1.409 −1.4465 −1.416 −1.446328 2.11E−06 0.00058884 down Zfp677 Protein Zfp677 Q6PFA2 −1.132 −0.575 −1.5885 −2.599 −1.473625 0.009403258 0.02774584 down Clta Clathrin light chain A Q6PGJ3 −1.156 −1.255 −1.2885 −1.61 −1.288063 1.15E−05 0.001090211 down L1cam L1 cell adhesion molecule Q6UQ17 1.126 1.134 1.7555 1.841 1.464125 0.000721174 0.005903461 up Atp8b3 Phospholipid-transporting ATPase IK Q6ZQL4 −1.562 −0.715 −0.9435 −1.351 −1.142875 0.001707317 0.009353658 down Wdr43 WD repeat-containing protein 43 Q6ZWN5 −1.072 −0.691 −1.1845 −2.085 −1.182848 0.001508063 0.008732383 down Rps9 40S ribosomal protein S9 Q6ZWR6 1.167 0.703 1.1985 1.566 1.168184 0.00033372 0.004094465 up Syne1 Nesprin-1 Q6ZWU9 −1.679 −1.427 −1.6985 −2.385 −1.697752 1.68E−05 0.001250999 down Rps27 40S ribosomal protein S27 Q6ZWV3 −1.298 −0.703 −1.0565 −1.537 −1.148625 0.000878643 0.006568512 down Rpl10 60S ribosomal protein L10 Q6ZWV7 −0.946 −0.202 −1.1305 −2.526 −1.127441 0.01909055 0.04529062 down Rpl35 60S ribosomal protein L35 Q6ZWY3 −1.59 −1.286 −1.4875 −2.317 −1.588919 7.65E−05 0.002167266 down Rps27l 40S ribosomal protein S27-like Q6ZWZ4 −1.085 −1.539 −0.8265 −2.058 −1.377125 0.002574063 0.01194031 down Rpl36 60S ribosomal protein L36 Q768S4 1.2 0.548 1.8455 1.859 1.363125 0.005000017 0.01819715 up Rph3al Rab effector Noc2 Q7JJ13 −1.243 −0.748 −0.9235 −1.666 −1.145125 0.00159883 0.009055139 down Brd2 Bromodomain-containing protein 2 Q7TNV0 −1.8 −0.726 −1.2915 −1.861 −1.419625 0.002021786 0.01030991 down Dek Protein DEK Q7TQD2 1.195 1.666 0.7645 1.337 1.240625 0.000541584 0.005190266 up Tppp Tubulin polymerization-promoting protein Q80SU7 −1.279 −0.758 −1.2235 −1.338 −1.223929 1.74E−05 0.001250999 down Gvin1 Interferon-induced very large GTPase 1 Q80TR4 1.316 1.587 1.2175 0.818 1.234625 0.000257518 0.003672153 up Slit1 Slit homolog 1 protein Q80V42 1.517 1.383 1.3355 1.228 1.365875 6.51E−06 0.000907306 up Cpm Carboxypeptidase M Q80XU3 −1.892 −0.72 −1.5225 −1.116 −1.312625 0.002412548 0.01144033 down Nucks1 Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 Q80Z37 1.31 0.914 1.7665 0.782 1.193125 0.002099592 0.01049665 up Topors E3 ubiquitin-protein ligase Topors Q80ZH7 −1.437 −0.415 −1.3725 −1.247 −1.2478 0.000104265 0.002461201 down Lig3 DNA ligase Q8BHB9 −1.576 −1.245 −1.3195 −1.01 −1.287625 6.39E−05 0.001993323 down Clic6 Chloride intracellular channel protein 6 Q8BK48 −1.646 −1.907 −2.1625 −1.046 −1.690375 0.000420689 0.004631048 down Ces2e Pyrethroid hydrolase Ces2e Q8BM96 −0.895 −1.193 −1.2285 −1.142 −1.142365 1.36E−05 0.001175119 down Gpr128 Probable G-protein coupled receptor 128 Q8BPQ7 1.5 0.707 1.4015 1.339 1.339562 2.35E−05 0.001402557 up Sgsm1 Small G protein signaling modulator 1 Q8BRB7 −0.966 −1.077 −1.3755 −1.962 −1.345125 0.000929521 0.00675869 down Kat6b Histone acetyltransferase KAT6B Q8BW75 −0.94 −1.056 −1.8625 −1.177 −1.176056 0.000201809 0.003273883 down Maob Amine oxidase [flavin-containing] B Q8BZ20 1.138 0.69 1.1465 1.295 1.138418 2.33E−05 0.001402557 up Parp12 Poly [ADP-ribose] polymerase 12 Q8C159 −0.633 −1.446 −1.1765 −1.271 −1.177491 0.000193952 0.003206267 down Ttc22 Tetratricopeptide repeat protein 22 Q8C196 −1.302 −0.76 −1.9525 −0.825 −1.209875 0.004336344 0.01660381 down Cps1 Carbamoyl-phosphate synthase [ammonia], mitochondrial Q8C2E4 −1.411 −1.637 −1.8825 −2.231 −1.790375 0.000103319 0.002461201 down Ptcd1 Pentatricopeptide repeat-containing protein 1, mitochondrial Q8C393 −1.644 −1.003 −1.1485 −2.908 −1.640816 0.004385833 0.01669742 down Zim1 Protein Zim1 Q8C407-2 −1.553 −0.796 −1.7055 −2.059 −1.554821 0.000542507 0.005190266 down Yipf4 Isoform 2 of Protein YIPF4 Q8C5N3 −1.581 −0.922 −0.9735 −1.648 −1.281125 0.001318049 0.008181909 down Cwc22 Pre-mRNA-splicing factor CWC22 homolog Q8CAB8 1.555 0.678 1.5715 1.494 1.494305 4.88E−06 0.000841369 up Gatsl2 GATS-like protein 2 Q8CFC7 −1.219 −0.633 −0.8625 −1.84 −1.138625 0.004300742 0.01651905 down Clasrp CLK4-associating serine/arginine rich protein Q8CGK7 −1.028 −1.1 −1.4805 −1.82 −1.357125 0.000583835 0.005353383 down Gnal Guanine nucleotide-binding protein G(olf) subunit alpha Q8CIV3 1.6 0.988 0.9025 1.225 1.178875 0.000434819 0.00471144 up Liph Lipase member H Q8K023 −1.063 −0.99 −1.9945 −1.758 −1.451375 0.002113455 0.01051355 down Akr1c18 Aldo-keto reductase family 1 member C18 Q8K1K3 −1.095 −0.395 −1.5935 −1.813 −1.224125 0.007199488 0.02306023 down Tinf2 TERF1-interacting nuclear factor 2 Q8K354 −1.154 −1.435 −1.8555 −0.441 −1.221375 0.004436258 0.01681909 down Cbr3 Carbonyl reductase [NADPH] 3 Q8K4B2 1.448 0.943 1.1955 1.204 1.197625 4.16E−05 0.001671268 up Irak3 Interleukin-1 receptor-associated kinase 3 Q8K4R4 1.072 0.913 1.6335 1.321 1.234875 0.000406991 0.004530039 up Pitpnc1 Cytoplasmic phosphatidylinositol transfer protein 1 Q8R0T2 −1.662 −0.647 −0.8365 −2.825 −1.492625 0.01850904 0.04426219 down Znf768 Zinc finger protein 768 Q8R550 1.738 1.082 1.8435 1.303 1.491625 0.000409113 0.004547344 up Sh3kbp1 SH3 domain-containing kinase-binding protein 1 Q8VCI0 −1.187 −1.193 −1.4105 −0.754 −1.187606 4.06E−05 0.001671268 down Plbd1 Phospholipase B-like 1 Q8VCT4 −1.923 −1.965 −2.3285 −1.001 −1.924169 4.73E−05 0.001721365 down Ces1d Carboxylesterase 1D Q8VE10 −1.74 −0.906 −0.8235 −1.246 −1.178875 0.001494738 0.0086887 down Naa40 N-alpha-acetyltransferase 40 Q8VE33 2.102 0.932 1.1705 1.609 1.453375 0.001660036 0.009251413 up Gdap1l1 Ganglioside-induced differentiation-associated protein 1- like 1 Q8VEE1 −1.327 −1.525 −1.0345 −1.145 −1.257875 8.60E−05 0.002281069 down Lmcd1 LIM and cysteine-rich domains protein 1 Q8VHB5 −1.611 −1.401 −1.7625 −1.754 −1.632125 8.58E−06 0.000977434 down Ca9 Carbonic anhydrase 9 Q8VHC3 1.688 1.48 1.1495 1.521 1.480691 1.53E−05 0.001188215 up Selm Selenoprotein M Q8VI93 1.378 0.979 1.6325 1.853 1.460625 0.000350804 0.004189781 up Oas3 2′-5′-oligoadenylate synthase 3 Q8WUR0 −0.949 −1.798 −1.4995 −1.811 −1.514375 0.000333673 0.004094465 down Protein C19orf12 homolog Q91UZ1 1.324 1.664 1.3895 1.329 1.389173 4.77E−06 0.000841369 up Plcb4 Phosphoinositide phospholipase C Q91VE6 −1.492 −1.242 −1.0275 −1.884 −1.411375 0.000379021 0.004362831 down Nifk MKI67 FHA domain-interacting nucleolar phosphoprotein Q91WA1 −1.929 −0.883 −1.5765 −2.303 −1.672875 0.001338945 0.00822481 down Tipin TIMELESS-interacting protein Q91WU0 −1.5 −1.991 −2.4445 −0.456 −1.597875 0.00675493 0.02198782 down Ces1f Expressed sequence AU018778 Q91Y74 −0.783 −1.258 −1.9425 −0.946 −1.232375 0.002374948 0.01134257 down St3gal4 CMP-N-acetylneuraminate-beta-galactosamide-alpha-2,3- sialyltransferase 4 Q920F6 −1.931 −0.989 −2.1915 −1.967 −1.931734 1.03E−05 0.001045334 down Smc1b Structural maintenance of chromosomes protein 1B Q921T2 1.233 1.176 1.0935 1.365 1.216875 1.09E−05 0.001077527 up Tor1aip1 Torsin-1A-interacting protein 1 Q921X9 1.535 1.138 1.0115 1.523 1.301875 0.000241925 0.003568078 up Pdia5 Protein disulfide-isomerase A5 Q99JP6-2 1.14 1.24 1.2235 0.76 1.140479 2.73E−05 0.001497233 up Homer3 Isoform 2 of Homer protein homolog 3 Q99K73 −1.189 −0.97 −1.1925 −1.663 −1.19191 3.94E−05 0.001660769 down Nrf1 Nrf1 protein Q99LD8 1.314 1.577 1.1265 1.14 1.289375 5.78E−05 0.001920568 up Ddah2 N(G),N(G)-dimethylarginine dimethylaminohydrolase 2 Q99LZ3 −1.61 −1.013 −0.7435 −1.481 −1.211875 0.001699239 0.009334681 down Gins4 DNA replication complex GINS protein SLD5 Q99M01 −0.869 −0.578 −1.7495 −1.486 −1.170625 0.006575054 0.02156753 down Fars2 Phenylalanine--tRNA ligase, mitochondrial Q99M54 −1.383 −1.488 −0.4185 −1.548 −1.383657 3.90E−05 0.001660769 down Cdca3 Cell division cycle-associated protein 3 Q99N50-2 1.685 1.299 1.0465 1.663 1.423375 0.000239004 0.003546996 up Sytl2 Isoform 2 of Synaptotagmin-like protein 2 Q99PG0 −1.606 −1.392 −2.1105 −1.558 −1.60531 1.43E−05 0.00118665 down Aadac Arylacetamide deacetylase Q9CPS7 −1.383 −1.226 −0.9215 −1.327 −1.22672 4.08E−05 0.001671268 down Pno1 RNA-binding protein PNO1 Q9CPY1 −0.801 −0.766 −2.0015 −1.543 −1.277875 0.006835104 0.02217673 down Mrpl51 39S ribosomal protein L51, mitochondrial Q9CQM8 −1.227 −1.156 −0.7795 −1.716 −1.219625 0.000506438 0.005016799 down Rpl21 60S ribosomal protein L21 Q9CQU5 −1.159 −0.699 −1.1625 −1.13 −1.130129 8.04E−06 0.000936704 down Zwint ZW10 interactor Q9CVI2 −1.385 −1.072 −1.0115 −1.275 −1.185875 6.50E−05 0.002009755 down Fam133b Protein FAM133B Q9CWY4 −0.742 −0.855 −1.6895 −1.387 −1.168375 0.003069459 0.01331816 down Gemin7 Gem-associated protein 7 Q9CXC3 −1.486 −0.854 −1.7905 −1.7 −1.487435 0.000245296 0.003578677 down Mgme1 Mitochondrial genome maintenance exonuclease 1 Q9CXS4 −1.106 −1.141 −0.9445 −1.649 −1.1404 5.35E−05 0.001847242 down Cenpv Centromere protein V Q9CY16 −1.217 −0.431 −1.1285 −1.28 −1.129101 6.80E−05 0.002044753 down Mrps28 28S ribosomal protein S28, mitochondrial Q9CZM2 −1.509 −1.064 −0.9865 −2.686 −1.50632 0.003373831 0.01416337 down Rpl15 60S ribosomal protein L15 Q9CZT6 −1.275 −0.965 −0.8705 −1.413 −1.130875 0.000363681 0.004285573 down Cmss1 Protein CMSS1 Q9D009 −0.836 −2.401 −2.1745 −2.621 −2.176266 0.000153481 0.002827569 down Lipt2 Putative lipoyltransferase 2, mitochondrial Q9D0I8 −1.405 −0.874 −1.2445 −1.908 −1.357875 0.000630576 0.00555018 down Mrto4 mRNA turnover protein 4 homolog Q9D1C1 −1.316 −0.925 −1.1505 −1.63 −1.255375 0.000241261 0.003567274 down Ube2c Ubiquitin-conjugating enzyme E2 C Q9D1R9 −1.153 −1.229 −1.5795 −4.242 −1.577598 0.001508024 0.008732383 down Rpl34 60S ribosomal protein L34 Q9D3P9 1.731 0.439 0.8595 2.111 1.285125 0.01757603 0.04276185 up Nts Neurotensin/neuromedin N Q9D6F4 0.695 0.98 1.4175 1.959 1.262875 0.003901759 0.01564194 up Gabra4 Gamma-aminobutyric acid receptor subunit alpha-4 Q9D6X6 1.521 1.393 0.7475 1.055 1.179125 0.000893457 0.006630399 up Prss23 Serine protease 23 Q9D816 0.664 1.318 0.5735 1.971 1.131625 0.01282542 0.03424754 up Cyp2c55 Cytochrome P450 2C55 Q9D8W7 −0.573 −1.182 −1.9045 −1.927 −1.396625 0.00575519 0.01980477 down Ociad2 OCIA domain-containing protein 2 Q9D937 −2.074 −1.942 −1.0675 −2.286 −1.943261 5.62E−05 0.001896735 down 1810009A15Rik MCG127334 Q9D9Z1 −1.473 −0.579 −0.8635 −1.605 −1.130125 0.005324851 0.01890712 down Knstrn Small kinetochore-associated protein Q9DA97 −0.99 −1.148 −0.7465 −2.635 −1.146583 0.001509696 0.008735526 down 14-Sep Septin-14 Q9DBG7 1.346 1.118 0.9025 1.401 1.191875 0.000150065 0.002816442 up Srpr Signal recognition particle receptor subunit alpha Q9DCS2 −0.849 −0.662 −1.6145 −1.557 −1.170625 0.004879838 0.01797906 down UPF0585 protein C16orf13 homolog Q9DCT8 1.983 1.517 0.9975 1.047 1.386125 0.001339267 0.00822481 up Crip2 Cysteine-rich protein 2 Q9DD24 1.266 0.97 1.6605 1.153 1.262375 0.000169716 0.003015752 up Wbp5 WW domain-binding protein 5 Q9EPC5 −2.063 −2.064 −2.2365 −2.196 −2.139875 5.65E−07 0.000496308 down Rbp7 Retinoid-binding protein 7 Q9EQ08 1.356 0.64 2.0045 1.075 1.268875 0.003329005 0.01402663 up Sgsh Heparan N-sulfatase Q9ERH4 −1.354 −0.911 −1.2565 −1.536 −1.264375 0.000110527 0.002493535 down Nusap1 Nucleolar and spindle-associated protein 1 Q9ERZ0 −1.833 −1.41 −1.0155 −1.185 −1.360875 0.000349173 0.004189781 down Hemgn Hemogen Q9ET22 1.451 1.159 1.3455 1.153 1.277125 2.51E−05 0.001438314 up Dpp7 Dipeptidyl peptidase 2 Q9JHJ8-2 −1.805 −1.83 −2.0845 −2.229 −1.987125 9.49E−06 0.001014302 down Icoslg Isoform 2 of ICOS ligand Q9JHT5 1.463 1.751 1.5015 0.056 1.46377 6.09E−05 0.001945377 up Ammecr1 AMME syndrome candidate gene 1 protein homolog Q9JIB0 −1.2 −1.555 −1.6355 −1.315 −1.426375 4.75E−05 0.001721365 down Rangrf Ran guanine nucleotide release factor Q9JJ78 −1.497 −0.959 −0.7695 −1.442 −1.166875 0.001339328 0.00822481 down Pbk Lymphokine-activated killer T-cell-originated protein kinase Q9JJI8 −1.888 −1.349 −1.3975 −2.169 −1.700875 0.000327819 0.004078484 down Rpl38 60S ribosomal protein L38 Q9JJK5 1.863 0.766 1.1435 2.005 1.444375 0.003924183 0.01565951 up Herpud1 Homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 1 protein Q9JMC3 1.758 0.805 1.3105 1.67 1.385875 0.00085966 0.006487114 up Dnaja4 DnaJ homolog subfamily A member 4 Q9JME5 −1.059 −1.31 −1.1945 −1.459 −1.255625 3.35E−05 0.001610318 down Ap3b2 AP-3 complex subunit beta-2 Q9JMH7 −1.209 −1.761 −1.8685 −1.601 −1.609875 5.68E−05 0.001896735 down Neu3 Sialidase-3 Q9QWG7 −1.032 −1.575 −1.8475 −0.115 −1.142375 0.01815782 0.04367251 down Sult1b1 Sulfotransferase family cytosolic 1B member 1 Q9QXD6 −1.892 −2.49 −2.2475 −0.495 −1.894604 0.001240745 0.007891529 down Fbp1 Fructose-1,6-bisphosphatase 1 Q9QXE2 0.861 1.509 1.4485 2.093 1.477875 0.000597171 0.005425997 up Poll DNA polymerase lambda Q9QXI6 −0.837 −1.599 −1.4195 −1.306 −1.307123 0.000160715 0.002914586 down Slc5a1 SGLT1 protein Q9QXV0 1.444 0.883 1.5975 1.172 1.274125 0.000377612 0.004361008 up Pcsk1n ProSAAS Q9QYB2 0.838 1.286 1.3505 1.402 1.286461 1.53E−05 0.001188215 up Dach1 Dachshund homolog 1 Q9QYY9 −1.109 −2.606 −2.0305 −0.87 −1.653875 0.007753165 0.02430902 down Adh4 Alcohol dehydrogenase 4 Q9R022 1.573 1.212 0.6885 1.141 1.153625 0.000527425 0.00512337 up Dnajc12 DnaJ homolog subfamily C member 12 Q9R098 1.864 1.188 0.7445 1.669 1.366375 0.002141273 0.01059924 up Hgfac Hepatocyte growth factor activator Q9R0M0 1.297 0.675 1.2135 1.732 1.229375 0.000821301 0.006349624 up Celsr2 Cadherin EGF LAG seven-pass G-type receptor 2 Q9R0Y5-2 1.269 1.279 1.5015 0.887 1.269655 3.24E−05 0.00159398 up Ak1 Isoform 2 of Adenylate kinase isoenzyme 1 Q9WU40-2 1.383 1.618 1.4435 1.027 1.383821 3.67E−05 0.001639477 up Lemd3 Isoform 2 of Inner nuclear membrane protein Man1 Q9WVJ3 1.348 0.221 2.1645 1.67 1.351154 0.009321278 0.02760315 up Cpq Carboxypeptidase Q Q9Z0L8 1.579 1.347 0.9735 1.555 1.363625 0.000123141 0.002582605 up Ggh Gamma-glutamyl hydrolase Q9Z0X4 −1.365 −1.277 −1.4205 −1.014 −1.277643 2.32E−05 0.001402557 down Pde3a cGMP-inhibited 3′,5′-cyclic phosphodiesterase A Q9Z1W8 −1.809 −1.665 −2.8885 −3.388 −2.437625 0.001836613 0.009721674 down Atp12a Potassium-transporting ATPase alpha chain 2 Q9Z2D6-2 1.46 1.467 1.3535 1.962 1.466713 3.97E−06 0.000776465 up Mecp2 Isoform B of Methyl-CpG-binding protein 2 Q9Z2V4 −0.756 −1.581 −2.0085 −1.158 −1.375875 0.002520321 0.01180471 down Pck1 Phosphoenolpyruvate carboxykinase, cytosolic [GTP] V9GX31 −0.954 −0.783 −1.1615 −1.904 −1.159861 0.001335846 0.00822481 down Gm12728 Uncharacterized protein Table 3B. (FIG. 7A Paneth & EE InVivo TF) M1-1 Log2 Median Normalized M1-2 Log2 Median Normalized M2-1 Log2 Median Normalized M2-2 Log2 Median Normalized Average log FC TF PC Nupr1 1.12 0.44 1.37 1.15 1.02 Foxa3 0.15 0.09 1.09 1.42 0.69 Tcf12 0.22 0.45 0.67 0.58 0.48 Lbh 0.38 0.41 0.45 0.47 0.43 Sox9 −0.04 0.36 0.31 −0.04 0.15 TF EEC Ets1 2.24 1.47 2.04 2.91 2.17 Insm1 1.48 1.77 1.95 2.36 1.89 Peg3 1.82 1.53 1.67 1.94 1.74 Maged1 0.67 0.61 1.16 0.86 0.83 Jun 0.35 0.22 0.34 0.21 0.28 Junb −0.07 −0.16 0.13 −0.17 −0.07

TABLE 4 Enrichments for gene ontology (GO) terms generated with the ENR+CD- enriched and ENR-enriched proteomes on a background of all identified proteins, performed in DAVID 6.8 Table 4A. ENR+CD BP ENR+CD-enriched Biological Process Count % Proteins log2(Fold Enrichment) −log10(FDR) Term 18  8.0 Q9R013, Q3UN27, Q9JJN5, P97449, Q80V42, Q8K0D2, Q00493, P06797, 1.37 2.07 proteolysis Q9ET22, Q9WVJ3, Q64191, O08529, Q61129, P63239, P98063, Q9D6X6, Q9R098, P18242 18  8.0 P17553, P21570, P46660, P97449, Q9WUA1, Q9QXS6, Q8CFE5, Q03172, 1.14 1.31 multicellular organism development Q8K0T2, Q9QYB2, P97802, Q80TR4, Q9R0M0, Q63ZV0, O35594, O09010, P98063, P48437 14  6.2 Q3UN27, Q9Z0L8, Q05421, Q80YQ1, P08228, P21460, P47877, P48756, 1.45 1.56 response to drug F8VQA4, P03958, P43883, O55042, P35441, Q76854, P10107 14  6.2 P17553, Q8K4B2, Q64338, D3Z3A8, B1AUY3, P47877, Q3V2R3, Q6ZPF3, 0.82 0.23 signal transduction Q03172, Q8R4S0, Q9Z1B3, Q8K4R4, Q9R0M0, P10107 13  5.8 P21570, P46660, P27577, P97449, Q9QXS6, Q6J9G1, P97802, Q80TR4, Q63ZV0, 0.74 0.11 cell differentiation O35594, Q5S006, P84086, P98063 12  5.3 P09240, P27577, Q80YQ1, P21460, P11276, Q3UTR7, Q06890, Q63ZV0, 1.28 0.82 positive regulation of cell Q9DCT8, P35441, Q3TMQ6, P48437, P28667 proliferation 10  4.4 E9PXE2, Q9Z1B3, P56716, Q03517, D3Z3A8, Q5S006, Q91UZ1, E9Q0S6, 0.89 0.11 intracellular signal transduction Q3V2R3, Q6ZPF3 9 4.0 P08551, O08599, Q3UTR7, P56695, Q08535, O55042, P28184, Q91ZZ3, P08228 2.19 1.95 negative regulation of neuron apoptotic process 7 3.1 D3YYS6, A0JNU3, Q9Z1B3, Q8CIV3, Q9Z0Y2, Q91UZ1, Q3TTY0 2.15 1.15 lipid catabolic process 7 3.1 P56695, Q80YQ1, Q9JJK5, P61961, P35441, Q921X9, P39654, D3Z6P0 2.15 1.15 response to endoplasmic reticulum stress 7 3.1 P21570, P03958, F8VQA4, O08529, P27577, P28184, P21460 1.54 0.38 response to hypoxia 7 3.1 Q3UN27, P03958, Q3UTR7, P97290, O55042, P08228, P47877 1.50 0.35 aging 6 2.7 Q9Z1B3, P52792, O08599, P63239, P55095, P48756 3.14 2.14 regulation of insulin secretion 6 2.7 Q9Z1B3, P08551, Q00896, P22599, P10107, P48756 2.65 1.43 response to peptide hormone 5 2.2 P08553, P08551, P19246, P46660, P08228 4.34 3.05 neurofilament cytoskeleton organization 5 2.2 Q9D848, P21460, Q8C1N8, Q5ERJ0, D3YX03 3.34 1.72 defense response 5 2.2 O88312, Q80YQ1, P35441, P39654, Q9QXS6, P37889 3.34 1.72 positive regulation of cell-substrate adhesion 5 2.2 P52792, Q06890, Q63ZV0, P10107, P48756 3.09 1.43 endocrine pancreas development 5 2.2 Q00896, O35684, P97290, P21460, P22599 2.88 1.19 negative regulation of peptidase activity 5 2.2 Q9ER67, Q3UTR7, P27577, P47877, P48756 2.53 0.82 female pregnancy 5 2.2 Q3UN27, P17897, P21570, Q9Z0Y2, P26339 2.53 0.82 defense response to Gram-positive bacterium 5 2.2 Q9JJN5, P63239, Q80V42, Q00493, P06797 2.39 0.68 protein processing 5 2.2 Q3UN27, P17897, Q8C1N8, D3YX02, Q3TMQ6 2.21 0.52 defense response to bacterium 5 2.2 A2AFS3, Q5S006, E9Q835, Q8C7E4, P06797 2.17 0.49 cellular response to starvation 5 2.2 F8VQA4, P27577, P21460, P47877, P10107 1.91 0.30 response to estradiol 5 2.2 O08599, Q5DQR4, P84086, E9Q835, Q76854 1.67 0.16 exocytosis 5 2.2 P08553, P08551, P14873, P19246, A2ARP8 1.53 0.10 microtubule cytoskeleton organization 4 1.8 P21570, Q9Z0Y2, Q45VN2, Q3TMQ6 3.70 1.33 antibacterial humoral response 4 1.8 F8VQA4, Q9JJN5, Q80V42, Q00493 3.56 1.20 peptide metabolic process 4 1.8 A0JNU3, Q9Z0Y2, O55042, Q3TTY0 3.21 0.90 phospholipid metabolic process 4 1.8 Q3UTR7, P27577, Q80YQ1, P35441, P48437 2.93 0.68 positive regulation of endothelial cell migration 4 1.8 Q8K4B2, P27577, O55042, P10107 2.77 0.56 response to interleukin-1 4 1.8 Q3UN27, P08228, P21460, P48437 2.77 0.56 response to nutrient levels 4 1.8 Q5S006, O55042, P28184, P26339 2.43 0.35 negative regulation of neuron death 4 1.8 F8VQA4, Q9JJN5, P47877, P06797 2.43 0.35 response to glucocorticoid 4 1.8 P08551, Q80TR4, Q06890, Q5S006 2.06 0.16 neuron projection morphogenesis 4 1.8 O09010, Q5S006, Q9JJK5, P55095 1.85 0.09 positive regulation of protein binding 3 1.3 P08553, P08551, P19246 5.02 1.35 neurofilament bundle assembly 3 1.3 P09240, P55095, P81117 4.60 1.07 negative regulation of appetite 3 1.3 P63239, Q9QXV0, P12961 4.60 1.07 peptide hormone processing 3 1.3 I1E4X8, P56695, Q3UP38 4.28 0.87 positive regulation of calcium ion transport 3 1.3 P08553, P08551, P19246 4.28 0.87 intermediate filament bundle assembly 3 1.3 P08553, P08551, P19246 4.02 0.71 axon development 3 1.3 Q3UN27, P27577, P10107 4.02 0.71 estrous cycle 3 1.3 Q5S006, P55200, P48756 3.60 0.49 exploration behavior 3 1.3 P56695, Q5S006, Q9JJK5 3.60 0.49 negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway 3 1.3 Q80YQ1, P35441, P10107, P11276 3.60 0.49 peptide cross-linking 3 1.3 B9EJ86, P21570, P28184 3.43 0.41 activation of protein kinase B activity 3 1.3 Q06890, Q5S006, O55042 3.43 0.41 regulation of neuron death 3 1.3 Q8CJ27, Q08535, P48437 3.28 0.35 neuronal stem cell population maintenance 3 1.3 P08553, P19246, P46660 3.14 0.29 intermediate filament cytoskeleton organization 3 1.3 P21570, P52792, Q80YQ1, P35441 3.02 0.24 positive regulation of phosphorylation 3 1.3 O55042, Q91ZZ3, Q810U3 2.80 0.17 synapse organization 3 1.3 D3YYS6, Q9D816, P39654 2.80 0.17 arachidonic acid metabolic process 3 1.3 P56716, P14873, A2ARP8 2.70 0.14 negative regulation of microtubule depolymerization 3 1.3 Q9WVJ3, P97449, Q00493 2.60 0.12 peptide catabolic process 3 1.3 Q3UN27, P17897, P26339 2.60 0.12 defense response to Gram-negative bacterium 3 1.3 Q3UTR7, P28184, P08228 2.52 0.09 positive regulation of catalytic activity 2 0.9 P08551, P19246 5.02 0.19 response to sodium arsenite 2 0.9 B2KG46, D3Z390 5.02 0.19 minus-end-directed organelle transport along microtubule 2 0.9 Q9Z1B3, Q3TTY0 5.02 0.19 positive regulation of acrosome reaction 2 0.9 P08553, P08551 5.02 0.19 intermediate filament polymerization or depolymerization 2 0.9 P08553, P08551 5.02 0.19 regulation of axon diameter 2 0.9 P21460, P11276 5.02 0.19 cell activation 2 0.9 B2KG46, D3Z390 5.02 0.19 microtubule anchoring at microtubule organizing center 2 0.9 O55042, P10107 5.02 0.19 negative regulation of exocytosis 2 0.9 P84086, P26339 5.02 0.19 mast cell degranulation 2 0.9 P70429, Q9JJV2 4.43 0.11 negative regulation of ruffle assembly 2 0.9 I1E4X8, Q3UP38 4.43 0.11 store-operated calcium entry 2 0.9 P10107, P12961 4.43 0.11 regulation of hormone secretion 2 0.9 P21570, Q3UTR7 4.43 0.11 activation of phospholipase C activity 2 0.9 Q5S006, Q9JJV2 4.43 0.11 regulation of synaptic vesicle exocytosis 2 0.9 Q5S006, O55042 4.43 0.11 regulation of locomotion 2 0.9 Q03157, P81117 4.43 0.11 negative regulation of cAMP biosynthetic process 2 0.9 Q80TR4, Q5S006 4.43 0.11 tangential migration from the subventricular zone to the olfactory bulb 2 0.9 P80560, Q60673 4.43 0.11 insulin secretion involved in cellular response to glucose stimulus 2 0.9 E9Q0S6, P11276 4.43 0.11 cell-substrate junction assembly Table 4B. ENR+CD CC ENR+CD-enriched Cellular Component Count % Proteins log2(Fold Enrichment) −log10(FDR) Term 66 29.3 P21570, Q9JJN5, Q9Z0Y2, P46660, Q80YQ1, P97449, P12265, P48036, P17897, Q62395, O88312, P50543, P22599, 2.48 30.31 extracellular space P26339, P07309, P55095, P18242, Q8VI93, P17553, Q45VN2, Q9Z0L8, P08228, P06797, P11276, Q9WVJ3, Q64191, O35684, P63239, Q9D848, P35441, Q07797, Q8C1N8, D3YX02, P81117, D3YX03, Q9R013, Q00896, Q03517, P09240, P47877, P48756, F8VQA4, Q80TR4, Q8CIV3, Q3UTR7, Q06890, Q5S006, O55042, Q3UQ28, P28184, Q3TMX5, Q5ERJ0, Q9R098, Q3UN27, P97290, Q9QXV0, P19467, P21460, Q80V42, Q00493, E9PXE2, P03958, Q61129, Q08535, P98063, Q3TMQ6, P10107 65 28.9 P21570, E9Q390, Q80YQ1, Q32NZ6, P97449, P12265, Q6ZPF3, P48036, P17897, Q9Z1B3, Q62395, O88310, 0.41 0.97 extracellular exosome O08529, Q8R258, P50543, Q9JJV2, P22599, P07309, P18242, Q9CQ89, A2AFS3, Q9Z0L8, E9Q9C6, P08228, P06797, P11276, Q8R2K3, Q9WVJ3, Q64191, O08599, Q571E4, O35684, P61961, P35441, Q9D6X6, Q07797, P28667, P81117, P37889, Q9R013, Q00896, Q60648, Q9EQ08, P14824, P47877, A2AM05, F8VQA4, Q9DBG7, Q3UTR7, Q06890, P00683, Q5S006, Q3UQ28, Q3UN27, P97290, Q9QXV0, P19467, P21460, Q80V42, Q00493, Q9ET22, Q61129, Q99LD8, Q8C7E4, Q810U3, P10107 60 26.7 P21570, Q9JJN5, Q9Z0Y2, Q80YQ1, A9Z1V5, P17897, Q62395, O88310, O88312, P22599, P07309, P26339, P55095, 2.61 29.37 extracellular region P18242, P17553, Q9Z0L8, P08228, P11276, Q9WVJ3, Q35684, P35441, Q9D6X6, Q07797, Q8C1N8, P37889, P81117, Q00896, Q03517, P09240, P47877, Q8K0D2, P48756, Q80TR4, Q8CIV3, Q06890, P16014, P00683, O55042, Q3UQ28, Q3TMX5, O88803, Q9R098, Q3UN27, Q91WD9, P97290, Q9QXV0, P19467, Q9WUA1, P21460, P47867, Q00493, P12961, Q9ET22, P97802, Q9D3P9, Q61129, Q08535, P98063, Q8C7E4, Q3TMQ6, P10107 45 20.0 A2AMT1, E9Q390, Q32M21, P59764, Q5DQR4, Q03157, Q9QXS6, Q69ZT9, Q6UQ17, Q5HZI2, P48036, Q9Z1B3, 0.38 0.35 plasma membrane Q6J9G1, F8VQA4, O88310, O08529, Q8CIV3, I1E4X8, Q5S006, O55042, P28184, Q8R2S8, Q8VI93, Q9EST1, Q9D6F4, Q8BY35, P14873, A2AFS3, Q60673, P19467, P08228, Q80V42, Q3TTY0, E9PXE2, P03958, O08599, D3Z390, Q9R0M0, P43883, Q99JA5, P39654, Q76854, Q810U3, P10107, P28667 30 13.3 Q00896, Q80YQ1, P12265, Q6UQ17, Q61263, P48036, B9EJ86, Q9DBG7, F8VQC7, O08529, I1E4X8, O88312, 0.81 1.43 endoplasmic reticulum Q06890, Q5S006, Q3UQ28, P22599, Q3TMX5, Q8K3Z9, D3Z6P0, P56695, Q05421, P21460, Q8VHC3, Q9WVJ3, Q64191, Q9D816, Q9JJK5, P35441, Q921X9, Q05186, P81117 28 12.4 P21570, Q8BPQ7, Q8R550, E9Q390, E9Q835, P47877, Q6UQ17, F8VQA4, Q06890, P80560, Q5S006, P26339, 1.57 5.12 cytoplasmic vesicle Q91WD9, B2KG46, Q60673, P08228, P47867, Q00493, P06797, Q9ET22, P03958, P97802, Q9D3P9, D3Z390, P63239, Q768S4, Q3TMQ6, P10107 27 12.0 Q8BPQ7, Q4VAH7, Q00896, Q91ZZ3, Q03157, Q6ZWR6, Q6UQ17, O08529, O09010, Q5S006, O55042, Q3UP38, 0.64 0.59 Golgi apparatus P22599, Q62431, B2KG46, Q60673, A2AFS3, Q9QXV0, B1AUY3, Q00493, Q8VHC3, Q9ET22, Q9WVJ3, D3Z390, Q9D5R3, P98063, P81117 19 8.4 Q03517, Q9Z0Y2, Q60673, Q9QXV0, Q80YQ1, Q5DQR4, P08228, P06797, P12961, Q00493, P17897, F8VQA4, 3.60 13.43 secretory P52792, Q62395, P16014, P80560, P35441, Q76854, P26339, Q3TMQ6 granule 17 7.6 Q9R013, A2AFS3, Q9Z0L8, Q9EQ08, Q60648, P08228, P12265, P21460, P06797, Q9ET22, Q9WVJ3, P03958, 1.71 3.14 lysosome Q64191, O08529, Q571E4, Q5S006, P18242 17 7.6 P21570, P09240, Q64338, P14873, Q60673, Q91ZZ3, P08228, P21460, Q90XS6, Q00493, P48756, P48036, F8VQA4, 1.36 1.95 neuronal P03958, Q9D3P9, Q5S006, P84086 cell body 14 6.2 Q9D6F4, Q91WD9, Q8R550, P14873, Q60673, E9Q835, Q91ZZ3, Q3V2R3, D3YYS6, P80560, Q5S006, P84086, 1.38 1.48 synapse O55042, Q9Z1S5 11 4.9 P48036, P08553, F8VQA4, P09240, P14873, P19246, Q60673, Q5S006, Q00493, P06797, P81117 2.73 4.25 perikaryon 11 4.9 D3YYS6, P08553, P08551, P09240, P14873, P19246, Q5S006, O55042, P28184, P21460, Q810U3 1.17 0.57 axon 11 4.9 P08553, F8VQA4, Q8R550, Q91WD9, P08551, Q06890, Q5S006, P08228, P06797, Q9Z1S5, D3Z710 0.91 0.23 neuron projection 10 4.4 P17553, Q3UN27, Q62395, Q80TR4, E9Q9C6, Q3UQ28, P98063, Q07797, P11276, P37889 2.67 3.59 proteinaceous extracellular matrix 10 4.4 P21570, P08551, Q06890, P14873, Q5S006, O55042, B1AUY3, Q91ZZ3, Q9QXS6, Q6ZPF3 1.86 1.69 growth cone 10 4.4 Q3UN27, Q06890, Q9DCT8, Q80YQ1, P35441, Q3UQ28, P08228, Q07797, P11276, P37889, P18242 1.52 1.02 extracellular matrix 9 4.0 Q9Z1B3, P08553, P08551, O08599, P19246, P46660, Q7TQD2, P08228, Q810U3 0.99 0.18 myelin sheath 8 3.6 O08599, P09240, P80560, Q5S006, P84086, O55042, Q91ZZ3, Q9JJV2 2.50 2.25 terminal bouton 7 3.1 F8VQA4, Q91WD9, Q60673, Q768S4, P26339, P47867, Q00493 3.99 4.56 transport vesicle membrane 7 3.1 P17553, P17897, P80560, P63239, Q921X9, D3Z6P0, Q05186 1.85 0.83 endoplasmic reticulum lumen 7 3.1 Q8K0T2, P56716, Q64338, O35594, Q91XQ0, Q69ZT9, P10107 1.46 0.38 cilium 6 2.7 Q8BPQ7, Q8R550, E9Q390, O55042, E9Q835, P10107 1.77 0.49 cytoplasmic vesicle membrane 6 2.7 P48036, Q60673, Q5S006, O55042, E9Q835, P28184 1.67 0.40 synaptic vesicle 5 2.2 P48036, Q9D3P9, Q60673, O55042, Q91ZZ3 2.36 0.75 axon terminus 5 2.2 Q3UTR7, Q06890, P97290, Q07797, P11276 2.15 0.55 blood microparticle 5 2.2 P08553, A2AMT1, P08551, P19246, P46660 1.92 0.38 intermediate filament 5 2.2 P48036, P03958, Q80YQ1, P35441, P97449, P06797 1.76 0.27 external side of plasma membrane 4 1.8 P08553, P08551, P19246, P46660 4.67 2.43 neurofilament 4 1.8 O88310, Q99JA5, Q8R2S8, Q80V42 3.09 0.90 anchored component of membrane 4 1.8 F8VQA4, P80560, Q768S4, Q00493 3.09 0.90 secretory granule membrane 4 1.8 Q5S006, O55042, P28184, Q91ZZ3 2.99 0.82 inclusion body 3 1.3 P63239, P55095, P48756 4.99 1.44 secretory granule lumen 3 1.3 Q03517, P08228, Q00493 4.58 1.15 dense core granule 3 1.3 P08553, Q06890, P19246 4.58 1.15 neurofibrillary tangle 3 1.3 P84086, P26339, P10107 3.99 0.79 mast cell granule 3 1.3 P03958, Q5S006, P08228 3.26 0.41 dendrite cytoplasm 3 1.3 O55042, Q6ZWR6, P81117 3.26 0.41 nuclear outer membrane 2 0.9 Q06890, P26339 4.99 0.25 chromaffin granule Table 4C. ENR+CD MF ENR+CD-enriched Molecular Function Count % Proteins log2(Fold Enrichment) −log10(FDR) Term 39  17.3 Q9R013, P21570, Q9JJN5, Q64338, Q9Z0Y2, Q60648, P97449, P12265, Q8K0D2, Q6UQ17, 0.63 1.19 hydrolase activity P17897, Q9Z1B3, A0JNU3, O08529, Q8CIV3, P80560, P00683, Q9R098, P18242, Q3UN27, Q9Z0L8, Q80V42, Q3TTY0, Q00493, P06797, D3YYS6, Q9WVJ3, Q9ET22, P03958, Q64191, P97802, Q61129, Q571E4, Q99LD8, P63239, Q9D6X6, P98063, Q8C7E4, Q3TMQ6 24  10.7 Q9Z0Y2, Q80YQ1, Q91UZ1, Q91ZZ3, P14824, Q8K0D2, Q5HZI2, P48036, Q9Z1B3, F8VQA4, 1.99 6.48 calcium ion binding O08529, I1E4X8, Q80TR4, O55042, P50543, Q3UP38, Q91WD9, Q9R0M0, P35441, Q768S4, P98063, P10107, Q05186, P81117, P37889 19  8.4 Q9R013, Q3UN27, Q9JJN5, Q9Z0L8, P97449, Q80V42, Q8K0D2, Q00493, P06797, Q9ET22, 1.61 3.23 peptidase activity Q9WVJ3, Q64191, O08529, Q61129, P63239, P98063, Q9D6X6, Q9R098, P18242 17  7.6 P08551, Q00896, Q8CAB8, P27577, G3X9H7, P08228, Q03157, P21460, P11276, P17897, 0.69 0.25 identical protein O08599, Q5S006, O55042, P55200, P22599, P07309, O88803 binding 12  5.3 P21570, P14873, D3Z3A8, Q5S006, A2ARP8, G3X9H7, E9Q0S6, P70429, Q9JJV2, Q9QXS6, 1.07 0.50 actin binding Q6ZWR6, P28667 11  4.9 Q9Z1B3, Q8BPQ7, F8WIA4, D3Z3A8, P59764, Q5S006, Q5DQR4, B1AUY3, Q3V2R3, Q69ZT9, 1.40 0.96 GTPase activator Q6ZPF3 activity 11  4.9 P17553, P21570, P08553, Q6J9G1, Q9Z0Y2, Q80TR4, Q08535, G3X9H7, P12265, Q6ZWR6, 1.30 0.77 receptor binding P48756 8 3.6 D3YYS6, E9PXE2, B9EJ86, Q8K4R4, E9Q835, P39654, P14824, D3Z6P0 1.05 0.14 lipid binding 7 3.1 Q3UN27, P21570, Q8CIV3, Q80TR4, Q80YQ1, P35441, Q03157, P11276 2.91 2.45 heparin binding 7 3.1 Q9WVJ3, Q3UN27, Q9JJN5, P97449, P98063, Q80V42, Q00493 2.11 1.16 metallopeptidase activity 7 3.1 Q8BPQ7, F8WIA4, B2KG46, D3Z390, Q5DQR4, Q768S4, Q69ZT9 1.31 0.23 Rab GTPase binding 6 2.7 Q3UTR7, P09240, Q08535, P07309, P55095, P48756 3.84 3.30 hormone activity 6 2.7 Q00896, Q3UTR7, O35684, P97290, Q9QXV0, P22599 3.06 2.08 serine-type endopeptidase inhibitor activity 6 2.7 P21570, F8VQA4, Q9CQ89, O55042, P28184, P08228 2.94 1.91 copper ion binding 6 2.7 Q9ET22, Q61129, P63239, Q9D6X6, Q8K0D2, Q9R098 2.60 1.44 serine-type peptidase activity 6 2.7 Q3UN27, Q61129, P63239, Q9D6X6, Q8K0D2, Q9R098 2.56 1.38 serine-type endopeptidase activity 6 2.7 P21570, P97802, P00683, Q5GAN1, Q8C7E4, Q3TMQ6 2.18 0.91 endonuclease activity 6 2.7 P08553, A2AMT1, P08551, P19246, P46660, P10107 1.45 0.21 structural molecule activity 5 2.2 P21570, P97802, Q5GAN1, Q8C7E4, Q3TMQ6 3.47 1.95 ribonuclease activity 5 2.2 Q00896, O35684, P97290, P21460, P22599 2.92 1.30 peptidase inhibitor activity 5 2.2 P56695, P84086, P50543, P14824, P10107 2.47 0.83 calcium-dependent protein binding 4 1.8 Q9ET22, Q9JJN5, Q80V42, Q00493 4.06 1.74 serine-type carboxypeptidase activity 4 1.8 Q00896, Q9QXV0, P21460, P22599 3.74 1.44 endopeptidase inhibitor activity 4 1.8 Q9WVJ3, Q9JJN5, Q80V42, Q00493 3.47 1.20 carboxypeptidase activity 4 1.8 P48036, P14824, P10107, Q5HZI2 2.97 0.78 calcium-dependent phospholipid binding 4 1.8 Q9WVJ3, Q9ET22, P97449, P06797 2.36 0.36 aminopeptidase activity 4 1.8 P08551, P19246, P10107, A2AM05 1.85 0.12 protein binding, bridging 3 1.3 Q9JJN5, Q80V42, Q00493 4.32 0.96 metallocarboxypeptidase activity 3 1.3 Q9Z1B3, Q921T2, Q6ZWR6 3.32 0.42 lamin binding 3 1.3 O08599, Q5S006, P84086 2.74 0.19 syntaxin-1 binding 3 1.3 Q61263, B9EJ86, P14824 2.64 0.16 cholesterol binding 3 1.3 A2CGA5, O55042, P28184 2.47 0.12 cysteine-type endopeptidase inhibitor activity involved in apoptotic process Table 4D. ENR BP ENR-enriched Biological Process Count % Proteins log2(Fold Enrichment) −log10(FDR) Term 30 14. 9 P62270, P27659, P61514, Q6ZWZ4, Q9CPY1, Q9D1R9, P61358, P62900, Q6ZWV3, Q642K5, Q9CQM8, 2.08 9.12 translation Q6ZWN5, Q99M01, P84099, Q6ZWU9, P62267, P62855, P62830, P62245, P67984, P62911, Q9CZM2, P62082, P14115, Q6ZWY3, P97351, Q9JJI8, P62889, Q6ZWV7, P25444 11 5.4 Q8BW75, P30681, Q8C196, Q9Z0X4, Q8VHB5, P11725, D3YU60, Q03311, E9QNX7, P27600, Q00623 1.27 0.66 response to drug 8 4.0 Q8BHB9, Q9Z1W8, E9Q8N8, J3QMG3, Q9QXI6, P56382, O35943, E9QNX7 1.39 0.40 ion transport 7 3.5 Q8CGK7, P51432, Q8BM96, Q3V3I2, Q8K023, P27600, Q00623 2.38 1.50 G-protein coupled receptor signaling pathway 5 2.5 Q6ZWZ4, D3YX71, P67984, P62900, Q9CZM2 3.05 1.38 cytoplasmic translation 5 2.5 P84244, Q7JJ13, P62806, P84228, Q8BRB7 2.38 0.68 nucleosome assembly 4 2.0 P06728, Q08652, Q9QYY9, Q00623 3.60 1.25 retinoid metabolic process 4 2.0 Q6ZWU9, P25444, Q6ZWY3, P62852 3.10 0.82 ribosomal small subunit assembly 4 2.0 Q9Z1W8, E9Q8N8, Q9QXI6, E9QNX7 2.79 0.59 sodium ion transport 3 1.5 P43137, Q8C196, P11725 5.18 1.47 midgut development 3 1.5 P06728, Q99PG0, Q00623 4.18 0.82 positive regulation of triglyceride catabolic process 3 1.5 P84244, P62806, P84228 3.96 0.69 positive regulation of gene expression, epigenetic 3 1.5 P84244, P62806, P84228 3.96 0.69 DNA methylation on cytosine 3 1.5 P02802, Q9Z1W8, P02798 3.96 0.69 response to metal ion 3 1.5 Q8C196, P06728, Q00623 3.31 0.37 triglyceride catabolic process 3 1.5 O35280, Q99LZ3, Q60997 3.18 0.32 inner cell mass cell proliferation 3 1.5 Q9QXI6, P55050, P48281 3.07 0.27 intestinal absorption 3 1.5 Q9CQU5, Q9D9Z1, Q9ERH4 2.77 0.17 mitotic sister chromatid segregation 3 1.5 P43137, P62889, P62911 2.68 0.14 liver regeneration 3 1.5 P27659, Q6ZWV3, Q9D0I8 2.60 0.12 ribosomal large subunit assembly 3 1.5 Q33DR2, P62806, P84228 2.60 0.12 protein heterotetramerization 3 1.5 P97328, E9Q1Q9, Q8C196, P11725 2.52 0.10 response to zinc ion 2 1.0 P02802, P02798 5.18 0.23 nitric oxide mediated signal transduction 2 1.0 Q8C196, P11725 5.18 0.23 anion homeostasis 2 1.0 P06728, Q00623 5.18 0.23 regulation of intestinal cholesterol absorption 2 1.0 Q91WU0, Q8VCT4 5.18 0.23 short-chain fatty acid catabolic process 2 1.0 P06728, Q00623 5.18 0.23 very-low-density lipoprotein particle remodeling 2 1.0 P06728, Q00623 5.18 0.23 high-density lipoprotein particle assembly 2 1.0 Q9CXS4, P84244 4.60 0.14 pericentric heterochromatin assembly 2 1.0 Q8C196, Q9Z2V4 4.60 0.14 cellular response to glucagon stimulus 2 1.0 P02772, Q8K023 4.60 0.14 progesterone metabolic process 2 1.0 E9QNS0, D3YYD0 4.60 0.14 negative regulation of immune response Table 4E. ENR CC ENR-enriched Cellular Component Count % Proteins log2(Fold Enrichment) −log10(FDR) Term 33 16.3 P62270, Q3UYK3, P27659, P61514, Q6ZWZ4, B1ARD6, P62900, Q9CQM8, F6R4Z5, Q6ZWN5, P84099, 0.84 1.83 intracellular B1ASD8, P62267, Q3UW68, Q8K023, B1B1D3, P51432, P55050, P67984, P62911, Q9CZM2, P62082, P14115, Q6ZWY3, P97351, P27600, Q6PEP4, Q9JJI8, P62889, Q8C393, Q9D0I8, Q60997, Q9JME5 27 13.4 P27659, Q6ZWZ4, Q9D1R9, O88554, Q6ZQL4, P62900, Q9CQM8, Q6ZWN5, P84099, Q8C196, P62267, 0.71 0.82 nucleolus P62855, P62830, E9Q5C9, Q3V1V3, P62852, P30681, Q9CPS7, P63166, P62082, Q91VE6, P97351, P40338, P09405, Q9ERH4, B1AX39, Q9D0I8 26 12.9 P62270, P27659, P61514, Q6ZWZ4, Q9CPY1, P62900, Q6ZWV3, Q642K5, Q9CQM8, Q6ZWN5, P84099, 2.59 11.19 ribosome P62267, P62855, P62245, P62852, P67984, Q9CY16, P62911, Q9CZM2, P62082, P14115, Q6ZWY3, P97351, Q9JJI8, P62889, P25444 26 12.9 P43137, P07310, Q91WU0, P02772, Q8VCT4, P63158, Q642K5, Q8VEE1, Q8VCI0, Q64176, E9PV38, O35280, 1.32 3.40 extracellular Q3V1V3, P30681, P06728, Q03311, O70514, Q8K354, E9QNX7, A2ARV4, Q6PDB7, Q8BK48, Q60997, Q00623, space D3YYD0, Q08ED5 24 11.9 P62270, P27659, Q6ZWZ4, P61514, Q9CPY1, P61358, P67984, P62900, Q9CQM8, P62911, Q9CY16, Q9CZM2, 1.65 4.64 intracellular P62082, Q6ZWN5, P14115, Q6ZWY3, P97351, Q9JJI8, P84099, P09405, P62889, P62267, P25444, P62852 ribonucleoprotein complex 20 9.9 P62270, P27659, P61514, Q61391, P61358, P67984, P62900, P62082, Q6ZWN5, P97314, P97351, P27600, 1.44 2.79 focal adhesion Q6PGJ3, P84099, Q9JJI8, P62889, P25444, P52800, A2APM2, P62830 18 8.9 P27659, Q6ZWZ4, P61514, Q9D1R9, P61358, P67984, P62900, Q9CQM8, Q6ZWV3, P62911, Q9CZM2, 3.60 12.49 cytosolic large P14115, Q9JJI8, P84099, D3YX71, P62889, Q6ZWV7, P62830 ribosomal subunit 12 5.9 P62270, Q6ZWU9, Q642K5, P62267, P62855, P62082, P25444, Q6ZWN5, P62245, P97351, Q6ZWY3, P62852 3.45 7.15 cytosolic small ribosomal subunit 12 5.9 Q9CXS4, P30681, Q9CQU5, P63158, Q9D9Z1, Q9ERH4, G3X956, O70126, Q91VE6, Q3UA16, Q920F6, Q8K1K3 1.02 0.45 chromosome 11 5.4 P62270, P62889, P61358, P67984, P62082, P62830, Q8VEE1, P62806, Q60997, P62245, P62852 1.85 1.96 extracellular matrix 7 3.5 P62270, Q642K5, P62267, P62855, P25444, Q6ZWN5, P62852 3.41 3.36 small ribosomal subunit 5 2.5 A2ARV4, Q60604, Q61391, Q9QXI6, B1AVH5 1.65 0.21 brush border 4 2.0 P84244, P62806, P84228, Q8BRB7 2.94 0.78 nucleosome 4 2.0 O35280, Q80ZH7, Q91VE6, Q920F6 2.33 0.36 condensed nuclear chromosome 3 1.5 P09405, Q6ZQL4, P63166 3.60 0.58 fibrillar center 3 1.5 Q8CGK7, Q3V3I2, P27600 2.86 0.25 heterotrimeric G-protein complex Table 4F. ENR MF ENR-enriched Molecular Function Count % Proteins log2(Fold Enrichment) −log10(FDR) Term 50 24.8 P62270, Q9CVI2, P61514, Q6ZQL4, P61358, Q9CQM8, Q52KI8, P62267, G3X956, P62855, Q80XU3, G3X8T2, 0.86 3.60 poly(A) RNA P62852, Q9CPS7, P67984, P62911, Q9CZM2, P14115, P97351, Q6ZWY3, P09405, Q9D0I8, P27659, Q6ZWZ4, binding Q7TNV0, P62900, Q642K5, Q6ZWV3, Q6ZWN5, P84099, Q64669, A2AR02, P62830, Q9CZT6, E9Q5K9, P62806, E9Q5C9, P62245, Q3V1V3, P30681, Q9CY16, P63166, P62082, Q91VE6, Q8R0T2, P62889, Q6ZWV7, B1AX39, Q9ERH4, P25444 31 15.3 P62270, P27659, P61514, Q6ZWZ4, Q9CPY1, Q9D1R9, P61358, P62900, Q6ZWV3, Q642K5, Q9CQM8, 2.82 15.74 structural Q6ZWN5, Q6ZWU9, P84099, D3YX71, P62267, P62855, P62830, P62245, P62852, P67984, P62911, Q9CZM2, constituent of P62082, P14115, Q6ZWY3, P97351, Q9JJI8, P62889, Q6ZWV7, P25444 ribosome 9 4.5 Q91WU0, Q8VCT4, Q6PDB7, E9PV38, Q99PG0, Q03311, Q8BK48, Q64176, Q08ED5 3.08 4.00 carboxylic ester hydrolase activity 7 3.5 E9Q8N8, P51162, Q3U9N9, Q9QXI6, P55050, Q08652, Q9EPC5 2.76 2.18 transporter activity 6 3.0 P84244, P09405, Q7TNV0, G3X956, P62806, P84228 1.56 0.28 histone binding 4 2.0 P84099, P61514, Q9D0I8, P62830 3.80 1.49 large ribosomal subunit rRNA binding 3 1.5 Q08652, Q9QYY9, Q9EPC5 4.71 1.20 retinol binding 3 1.5 Q9QYY9, O88451, Q8K023 3.90 0.71 retinol dehydrogenase activity 3 1.5 Q8CGK7, Q3V3I2, P27600 3.25 0.39 guanyl nucleotide binding 3 1.5 Q8CGK7, Q3V3I2, P27600 3.12 0.33 G-protein beta/gamma- subunit complex binding 2 1.0 Q9Z1W8, E9QNX7 5.12 0.26 hydrogen:potassium- exchanging ATPase activity 2 1.0 P06728, Q00623 5.12 0.26 phosphatidylcholine- sterol O- acyltransferase activator activity 2 1.0 Q08652, Q9EPC5 4.54 0.16 retinoid binding

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Various modifications and variations of the described methods, pharmaceutical compositions, and kits of the invention will be apparent to those skilled in the art without departing from the scope and spirit of the invention. Although the invention has been described in connection with specific embodiments, it will be understood that it is capable of further modifications and that the invention as claimed should not be unduly limited to such specific embodiments. Indeed, various modifications of the described modes for carrying out the invention that are obvious to those skilled in the art are intended to be within the scope of the invention. This application is intended to cover any variations, uses, or adaptations of the invention following, in general, the principles of the invention and including such departures from the present disclosure come within known customary practice within the art to which the invention pertains and may be applied to the essential features herein before set forth. 

1. A method of generating an ex vivo cell-based system that faithfully recapitulates an in vivo phenotype of interest comprising: a) determining, using single cell RNA sequencing, one or more cell types or one or more cell states in an initial cell-based system; b) identifying differences in one or more cell types and/or cell states between the initial cell-based system and a target in vivo system having the phenotype of interest, preferably, wherein identifying differences comprises comparing a gene expression distribution as determined by single cell RNA sequencing of the initial cell-based system and a gene expression distribution as determined by single cell RNA sequencing; and c) modulating the initial cell-based system to induce a shift in cell type and/or cell states that reduces the distance in gene expression space between the initial cell-based system and the in vivo system, preferably, wherein the distance is measured by a Euclidean distance, Pearson coefficient, Spearman coefficient, or combination thereof.
 2. The method of claim 1, wherein the gene expression space comprises 10 or more genes, 20 or more genes, 30 or more genes, 40 or more genes, 50 or more genes, 100 or more genes, 500 or more genes, or 1000 or more genes; or wherein the expression space defines one or more cell pathways; or wherein the expression space is a transcriptome of the target in vivo system.
 3. (canceled)
 4. (canceled)
 5. (canceled)
 6. (canceled)
 7. The method of claim 1, wherein the shift in cell type and/or cell states that reduces the distance in gene expression space in the initial cell-based system is a statistically significant shift in the gene expression distribution of the initial cell-based system toward that of the in vivo system, preferably, wherein the statistically significant shift is at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%.
 8. (canceled)
 9. The method of claim 7, wherein comparing a gene expression distribution comprises comparing the initial cells with the lowest statistically significant shift as compared to the in vivo system.
 10. The method of claim 1, further comprising modulating the initial cell-based system to induce a gain of function in addition to the in vivo phenotype of interest comprising modulating expression of one or more genes, gene expression cassettes, or gene expression signatures associated with the gain of function; or further comprising modulating the initial cell-based system to induce a loss of function in addition to the in vivo phenotype of interest comprising modulating expression of one or more genes, gene expression cassettes, or gene expression signatures associated with the loss of function.
 11. (canceled)
 12. The method claim 1, wherein modulating comprises increasing or decreasing expression of one or more genes, gene expression cassettes, or gene expression signatures; or wherein modulating comprises activating or inhibiting one or more genes, gene expression cassettes, or gene expression signatures.
 13. (canceled)
 14. The method of claim 1, wherein the initial cell-based system comprises a single cell type or subtype, a combination of cell types and/or subtypes, cell-based therapeutic, an explant, or an organoid, preferably, wherein the single cell type or subtype or combination of cell types and/or subtypes comprises an immune cell, intestinal cell, liver cell, kidney cell, lung cell, brain cell, epithelial cell, endoderm cell, neuron, ectoderm cell, islet cell, acinar cell, oocyte sperm, hematopoietic cell, hepatocyte, skin/keratinocyte, melanocyte, bone/osteocyte, hair/dermal papilla cell, cartilage/chondrocyte, fat cell/adipocyte, skeletal muscular cell, endothelium cell, cardiac muscle/cardiomyocyte, trophoblast, tumor cell, or tumor microenvironment (TME) cell; or wherein the single cell type or sub-type is pluripotent, or the combination of cell types and/or subtypes comprises one or more stem cells, more preferably, wherein the one or more stem cells are selected from the group consisting of lymphoid stem cells, myeloid stem cells, neural stem cells, skeletal muscle satellite cells, epithelial stem cells, endodermal and neuroectodermal stem cells, germ cells, extraembryonic and embryonic stem cells, mesenchymal stem cells, intestinal stem cells, embryonic stem cells, and induced pluripotent stem cells (iPSCs); or wherein the cell-based therapy comprises iPSCs, autologous T cells, CAR T cells, suppressive T cells or tissue transplants.
 15. (canceled)
 16. (canceled)
 17. (canceled)
 18. (canceled)
 19. The method of claim 14, wherein the initial cell-based system is derived from a subject with a disease, preferably, wherein the disease is selected from the group consisting of cancer, autoimmune disease, bone marrow failure, hematological conditions, aplastic anemia, beta-thalassemia, diabetes motor neuron disease, Parkinson's disease, spinal cord injury, muscular dystrophy, kidney disease, liver disease, multiple sclerosis, congestive heart failure, head trauma, lung disease, psoriasis, liver cirrhosis, vision loss, cystic fibrosis, hepatitis C virus, human immunodeficiency virus, inflammatory bowel disease (IBD), and any disorder associated with tissue degeneration.
 20. (canceled)
 21. The method of claim 1, wherein modulating the initial cell-based system comprises delivering one or more modulating agents that modify expression of one or more cell types or states in the initial cell-based system, delivering an additional cell type or sub-type to the initial cell-based system, or depleting an existing cell type or sub-type from the initial cell-based system, preferably, wherein the one or more modulating agents comprise one or more cytokines, growth factors, hormones, transcription factors, metabolites or small molecules; or wherein the one or more modulating agents are a genetic modifying agent or an epigenetic modifying agent.
 22. (canceled)
 23. (canceled)
 24. The method of claim 21, wherein the genetic modifying agent comprises a CRISPR system, a zinc finger nuclease system, a TALEN, or a meganuclease; or wherein the epigenetic modifying agent comprises a DNA methylation inhibitor, HDAC inhibitor, histone acetylation inhibitor, histone methylation inhibitor or histone demethylase inhibitor.
 25. (canceled)
 26. The method of claim 21, wherein the one or more modulating agents modulate one or more cell-signaling pathways, preferably, wherein the one or more pathways comprise Notch signaling; and/or wherein the one or pathways comprise Wnt signaling.
 27. (canceled)
 28. (canceled)
 29. The method of claim 26, wherein the initial cell-based system comprises Paneth cells and the one or more agents comprise a Wnt signaling activator and Notch signaling inhibitor, preferably, wherein the Wnt signaling activator comprises CHIR99021; and/or wherein the Notch signaling inhibitor comprises DAPT.
 30. (canceled)
 31. (canceled)
 32. The method of claim 1, further comprising: a) transplanting the initial cell-based system into an animal model; b) recovering cells from the transplanted cell-based system; c) performing single cell RNA sequencing on the recovered cells; and d) measuring statistically significant shifts in gene expression distribution compared to the in vivo system.
 33. An ex vivo cell-based system derived from claim
 1. 34. Use of the cell based system of claim 33 to identify a therapeutic agent or determine the efficacy of a therapeutic agent; or to select one or more therapeutic agents for treatment of a subject in need thereof; or to screen for one or more on-target or off-target genetic modifications.
 35. (canceled)
 36. (canceled)
 37. The ex vivo cell-based system of claim 33, wherein the initial cell-based system comprises a tumor cell; or wherein the initial cell-based system comprises a tumor microenvironment cell, preferably, wherein the tumor microenvironment cell is a tumor infiltrating lymphocyte (TIL).
 38. (canceled)
 39. (canceled)
 40. The system of claim 37, wherein the initial cell-based system comprises a single cell type or subtype or combination of cell types and/or subtypes that faithfully recapitulates a phenotype from a subject responsive to cancer treatment; or wherein the initial cell-based system comprises a single cell type or subtype or combination of cell types and/or subtypes that faithfully recapitulates a phenotype from a subject non-responsive to cancer treatment; or wherein the initial cell-based system comprises a single cell type or subtype or combination of cell types and/or subtypes that faithfully recapitulates a phenotype from a subject with a cancer recurrence.
 41. (canceled)
 42. The system of claim 40, wherein the treatment is an immunotherapy, preferably, wherein the immunotherapy is checkpoint blockade therapy.
 43. (canceled)
 44. (canceled)
 45. The ex vivo cell-based system of claim 33, wherein the initial cell-based system comprises an in vitro fertilized egg that faithfully recapitulates the phenotype of an in vivo fertilized egg.
 46. The ex vivo cell-based system of claim 33, wherein the system is an organoid model selected from the group consisting of an intestinal, liver, kidney, lung, or brain organoid model.
 47. Use of the system of claim 33 in a method for adoptive cell transfer (ACT), wherein a single cell type or subtype or combination of cell types and/or subtypes from the ex vivo cell-based system are transferred to a subject in need thereof, preferably, wherein the subject has disease selected from the group consisting of cancer, autoimmune disease, bone marrow failure, hematological conditions, aplastic anemia, beta-thalassemia, diabetes, motor neuron disease, Parkinson's disease, spinal cord injury, muscular dystrophy, kidney disease, liver disease, multiple sclerosis, congestive heart failure, head trauma, lung disease, psoriasis, liver cirrhosis, vision loss, cystic fibrosis, hepatitis C virus, human immunodeficiency virus, inflammatory bowel disease (IBD), and any disorder associated with tissue degeneration.
 48. (canceled)
 49. The method of claim 47, wherein T cells that faithfully recapitulate an in vivo phenotype of interest are transferred to a subject suffering from cancer; or wherein cells for regenerating a tissue are transferred.
 50. (canceled)
 51. Use of the system of claim 37 in a method for screening modulating agents; or for screening agents having antitumor activity.
 52. (canceled)
 53. The method of claim 51, wherein cancer cells are screened for agents capable of modulating an immune evasion phenotype; or wherein immune cells are screened for antitumor cell activity.
 54. (canceled)
 55. A method of screening for agents capable of modulating Paneth cell activity comprising: a) treating EGF, Noggin, R-spondin 1, CHIR99021 and DAPT (ENR+CD) cells with a stimulant capable of inducing Paneth cell secretion and an agent; and b) measuring Paneth cell antimicrobial secretion, or a) suspending EGF, Noggin, R-spondin 1, CHIR99021 and DAPT (ENR+CD) cells with bacteria and an agent; and b) measuring bacterial growth.
 56. (canceled)
 57. A method of producing an in vitro Paneth cell enriched gut organoid system comprising: a) culturing an LGR5+ ISC-enriched population of cells in a hydrogel matrix in the presence of EGF, Noggin, R-spondin 1, CHIR99021 and valproic acid (ENR+CV); b) culturing the ENR+CV cells in the presence of EGF, Noggin, R-spondin 1, CHIR99021 and DAPT (ENR+CD); and c) modulating the activity of one or more nuclear receptors selected from the group consisting of progesterone receptor (PR), aldosterone receptor (AR) and glucocorticoid receptor (GR).
 58. A cell obtained from by the method of claim
 57. 